Enzyme quantification

ABSTRACT

The invention generally relates to methods for quantifying an amount of enzyme molecules. Systems and methods of the invention are provided for measuring an amount of target by forming a plurality of fluid partitions, a subset of which include the target, performing an enzyme-catalyzed reaction in the subset, and detecting the number of partitions in the subset. The amount of target can be determined based on the detected number.

FIELD OF INVENTION

The present invention generally relates to droplet libraries and tosystems and methods for the formation of libraries of droplets. Thepresent invention also relates to methods utilizing these dropletlibraries in various biological, chemical, or diagnostic assays.

BACKGROUND

The manipulation of fluids to form fluid streams of desiredconfiguration, discontinuous fluid streams, droplets, particles,dispersions, etc., for purposes of fluid delivery, product manufacture,analysis, and the like, is a relatively well-studied art. Microfluidicsystems have been described in a variety of contexts, typically in thecontext of miniaturized laboratory (e.g., clinical) analysis. Other useshave been described as well. For example, International PatentApplication Publication Nos. WO 01/89788; WO 2006/040551; WO2006/040554; WO 2004/002627; WO 2008/063227; WO 2004/091763; WO2005/021151; WO 2006/096571; WO 2007/089541; WO 2007/081385 and WO2008/063227.

Precision manipulation of streams of fluids with microfluidic devices isrevolutionizing many fluid-based technologies. Networks of smallchannels are a flexible platform for the precision manipulation of smallamounts of fluids. However, virtually all microfluidic devices are basedon flows of streams of fluids; this sets a limit on the smallest volumeof reagent that can effectively be used because of the contaminatingeffects of diffusion and surface adsorption. As the dimensions of smallvolumes shrink, diffusion becomes the dominant mechanism for mixing,leading to dispersion of reactants; moreover, surface adsorption ofreactants, while small, can be highly detrimental when theconcentrations are low and volumes are small. As a result, currentmicrofluidic technologies cannot be reliably used for applicationsinvolving minute quantities of reagent; for example, bioassays on singlecells or library searches involving single beads are not easilyperformed. An alternate approach that overcomes these limitations is theuse of aqueous droplets in an immiscible carrier fluid; these provide awell-defined, encapsulated microenvironment that eliminates crosscontamination or changes in concentration due to diffusion or surfaceinteractions. Droplets provide the ideal microcapsule that can isolatereactive materials, cells, or small particles for further manipulationand study. However, essentially all enabling technology for microfluidicsystems developed thus far has focused on single phase fluid flow andthere are few equivalent active means to manipulate droplets requiringthe development of droplet handling technology. While significantadvances have been made in dynamics at the macro- or microfluidic scale,improved techniques and the results of these techniques are stillneeded. For example, as the scale of these reactors shrinks,contamination effects due to surface adsorption and diffusion limit thesmallest quantities that can be used. Confinement of reagents indroplets in an immiscible carrier fluid overcomes these limitations, butdemands new fluid-handling technology.

The present invention overcomes the current limitations in the field byproviding precise, well-defined, droplet libraries which can be utilizedalone, or within microfluidic channels and devices, to perform variousbiological and chemical assays efficiently and effectively, especiallyat high speeds.

SUMMARY

This invention provides methods to identify and quantify the presence,type, and amount of reactants and products of chemical reactions. Theinvention takes advantage of the ability to form discrete droplets thatcontain the components of a chemical reaction. Because measurements canbe performed on individual droplets and collections of individualdroplet, it is possible to identify and quantify chemical reactioncomponents in the droplets according to methods described herein.Methods of the invention are useful to detect and/or quantify anycomponent of a chemical reaction. In one preferred embodiment, enzymemolecules are quantified based on their activity inside individualdroplets. In order to identify and quantitate enzyme activity, dropletsare identified as “negative” and/or “positive” droplets for the reactioncatalyzed by the target enzyme, and the number of enzyme moleculeswithin positive droplets (e.g., based on the quantized signal strength)is determined. Digital counting of enzyme molecules provides anextremely wide dynamic range of detection, with a lower limit ofdetection dependent on the number of molecules available to count andthe total number of droplets read (e.g. 1 in 10⁷, in one hour using adroplet flow rate of 10⁷ per hour) and the upper limit for singlemolecule counting determined by the number of droplets but also includesa further range where multiple or average numbers of molecules arepresent in droplets.

In general, the invention involves incorporating components of achemical reaction in a droplet and allowing the chemical reaction tooccur in the droplet. One or more of the components of the reaction isdetectably labeled (e.g., with a reporter molecule) such that label isdetectable as a result of the reaction (e.g., release of a reporter).Detection and quantification of the label allows detection andquantification of the reaction components. The reporter moiety may beany detectable moiety that can be used as an indicator of reactioncomponents (e.g., enzyme activity). Any reporter system known in the artmay be used with methods of the invention. In certain embodiments, thereporter moiety is a fluorescent moiety.

In a preferred embodiment, a reporter is attached to one or moresubstrate(s) of a chemical reaction in a droplet, which label isreleased upon enzymatic catalysis. The number of droplets containingquantified enzyme molecules are then determined based upon the presenceand/or signal strength of the reporter. Reporter (and therefore enzyme)can be quantified based upon these measurements as well. Methods of theinvention involve forming a sample droplet. Any technique known in theart for forming sample droplets may be used with methods of theinvention. An exemplary method involves flowing a stream of sample fluidso that the sample stream intersects one or more opposing streams offlowing carrier fluid. The carrier fluid is immiscible with the samplefluid. Intersection of the sample fluid with the two opposing streams offlowing carrier fluid results in partitioning of the sample fluid intoindividual sample droplets. The carrier fluid may be any fluid that isimmiscible with the sample fluid. An exemplary carrier fluid is oil,which may in some cases be fluorinated. In certain embodiments, thecarrier fluid includes a surfactant, such as a fluorosurfactant.

In some aspects, the invention provides methods for digital distributionassays that allow, for example, for detection of a physiologicalcondition in a human. Detectable physiological conditions includeconditions associated with aggregation of proteins or other targets.Methods include forming fluid partitions that include components of adetectable chemical reaction and conducting the reaction. A distributionof at least one of the components is determined based on detecting thedetectable reaction. A statistically expected distribution can becomputed and compared to the determined distribution or comparisons ofdistributions from known or typical samples. Based on these comparisons,the presence and/or the severity of the potential condition can bedetermined. In certain embodiments, the condition involves proteinaggregation. The protein can be a protein from a sample from a patient.In some embodiments, methods assay for Alzheimer's disease, Parkinson'sdisease, Huntington's disease, Type II diabeties mellitus,prion-associated diseases, or other conditions.

Another droplet formation method includes merging at least two droplets,in which each droplet includes different material. Another dropletformation method includes forming a droplet from a sample, andcontacting the droplet with a fluid stream, in which a portion of thefluid stream integrates with the droplet to form a droplet. An electricfield may be applied to the droplet and the fluid stream. The electricfield assists in rupturing the interface separating the two fluids. Inparticular embodiments, the electric field is a high-frequency electricfield.

Methods of the invention may be conducted in microfluidic channels. Assuch, in certain embodiments, methods of the invention may furtherinvolve flowing the droplet channels and under microfluidic control.

BRIEF DESCRIPTION OF THE DRAWINGS

Non-limiting embodiments of the present invention will be described byway of example with reference to the accompanying drawings, which areschematic and are not intended to be drawn to scale. In the drawings,each identical or nearly identical component illustrated is typicallyrepresented by a single numeral. For the purposes of clarity, not everycomponent is labeled in every drawing, nor is every component of eachembodiment of the invention shown where illustration is not necessary toallow those of ordinary skill in the art to understand the invention. Inthe drawings:

FIG. 1 is an schematic illustrating the interacting modules of amicrofluidic device of the present invention.

FIG. 2 is a schematic illustrating a one emulsion library.

FIG. 3 is a schematic illustrating an antibody pair library for ELISAApplication.

FIG. 4 Panel A is a schematic illustrating that the cell in theProtein-Fragment Complementation Assay is not secreting any antigenhence the fluorogenic substrate is not converted into a fluorescentproduct. Panel B is a schematic showing the conversion to a fluorescentproduct.

FIG. 5 Panel A is a photograph showing droplets containing AmmoniumCarboxylate Salt of Krytox 157 FSH 2 Wt % in FC 3283 without PEG aminesalt. Panel B is a photograph showing droplets containing PEG 600Diammonium Carboxylate Salt of Krytox 157 FSH at 4.0% by volume.

FIG. 6 is a schematic illustrating a primer library generation.

FIG. 7 is a schematic illustrating enzyme amplified flow cytometry.

FIGS. 8A-8G show droplet formation and detection of reaction positivedroplets.

FIGS. 9A-9D show readouts of time traces at different enzymeconcentrations. Time traces show digital reactions in droplets at lowenzyme concentrations.

FIGS. 10A-10D show readouts of histograms. Increasing enzymeconcentrations shifts the distribution from quantized to average regime.

FIGS. 11A and 11B illustrate concentration determination using digitaldroplet data. Digital counting measurement of enzyme concentrationmatches known starting amount.

FIG. 12 is a schematic showing sandwich formation for digital dropletELISA.

FIGS. 13A-13D illustrates different digital droplet ELISA readoutcounting modes.

FIGS. 14A and 14B show embodiments for multiplexing digital assay.

FIGS. 15A and 15B show fluorescent polarization as another mode forreadout.

FIGS. 16A and 16B illustrate localized florescence as another mode forreadout.

FIG. 17 is illustrates a digital competitive allele specific enzyme(CASE) assay.

FIGS. 18A-18C show multiplexing embodiments.

FIGS. 19A and 19B show a workflow for a localized fluorescence bindingassay.

FIG. 20 shows monocyte detection according to certain embodiments.

FIGS. 21A-21C illustrate single droplet traces including optical labels.

FIGS. 22A-22C give single droplet traces with a scatter plot andhistogram.

FIGS. 23A-23C diagram adjusting a dynamic range of a localizedfluorescence assay.

FIG. 24 is a drawing showing a device for droplet formation.

FIG. 25 is a drawing showing a device for droplet formation.

FIG. 26 is a diagram of results of a digital distribution assay.

DETAILED DESCRIPTION

Droplet Libraries

Droplet libraries are useful to perform large numbers of assays whileconsuming only limited amounts of reagents. A “droplet,” as used herein,is an isolated portion of a first fluid that completely surrounded by asecond fluid. In some cases, the droplets may be spherical orsubstantially spherical; however, in other cases, the droplets may benon-spherical, for example, the droplets may have the appearance of“blobs” or other irregular shapes, for instance, depending on theexternal environment. As used herein, a first entity is “surrounded” bya second entity if a closed loop can be drawn or idealized around thefirst entity through only the second entity.

In general, a droplet library is made up of a number of library elementsthat are pooled together in a single collection. Libraries may vary incomplexity from a single library element to 10¹⁵ library elements ormore. Each library element is one or more given components at a fixedconcentration. The element may be, but is not limited to, cells, virus,bacteria, yeast, beads, amino acids, proteins, polypeptides, nucleicacids, polynucleotides or small molecule chemical compounds. The elementmay contain an identifier such as a label. The terms “droplet library”or “droplet libraries” are also referred to herein as an “emulsionlibrary” or “emulsion libraries.” These terms are used interchangeablythroughout the specification.

A cell library element can include, but is not limited to, hybridomas,B-cells, primary cells, cultured cell lines, cancer cells, stem cells,or any other cell type. Cellular library elements are prepared byencapsulating a number of cells from one to tens of thousands inindividual droplets. The number of cells encapsulated is usually givenby Poisson statistics from the number density of cells and volume of thedroplet. However, in some cases the number deviates from Poissonstatistics as described in Edd et al., “Controlled encapsulation ofsingle-cells into monodisperse picolitre drops” Lab Chip,8(8):1262-1264, 2008. The discreet nature of cells allows for librariesto be prepared in mass with a plurality of cellular variants all presentin a single starting media and then that media is broken up intoindividual droplet capsules that contain at most one cell. Theseindividual droplets capsules are then combined or pooled to form alibrary consisting of unique library elements. Cell division subsequentto, or in some embodiments following, encapsulation produces a clonallibrary element.

A bead based library element contains one or more beads, of a given typeand may also contain other reagents, such as antibodies, enzymes orother proteins. In the case where all library elements contain differenttypes of beads, but the same surrounding media, the library elements canall be prepared from a single starting fluid or have a variety ofstarting fluids. In the case of cellular libraries prepared in mass froma collection of variants, such as genomically modified, yeast orbacteria cells, the library elements will be prepared from a variety ofstarting fluids.

Often it is desirable to have exactly one cell per droplet with only afew droplets containing more than one cell when starting with aplurality of cells or yeast or bacteria, engineered to produce variantson a protein. In some cases, variations from Poisson statistics can beachieved to provide an enhanced loading of droplets such that there aremore droplets with exactly one cell per droplet and few exceptions ofempty droplets or droplets containing more than one cell.

Examples of droplet libraries are collections of droplets that havedifferent contents, ranging from beads, cells, small molecules, DNA,primers, antibodies. The droplets range in size from roughly 0.5 micronto 500 micron in diameter, which corresponds to about 1 pico liter to 1nano liter. However, droplets can be as small as 5 microns and as largeas 500 microns. Preferably, the droplets are at less than 100 microns,about 1 micron to about 100 microns in diameter. The most preferred sizeis about 20 to 40 microns in diameter (10 to 100 picoliters). Thepreferred properties examined of droplet libraries include osmoticpressure balance, uniform size, and size ranges.

The droplets comprised within the droplet library provided by theinstant invention are uniform in size. That is, the diameter of anydroplet within the library will vary less than 5%, 4%, 3%, 2%, 1% or0.5% when compared to the diameter of other droplets within the samelibrary. The uniform size of the droplets in the library is critical tomaintain the stability and integrity of the droplets and is alsoessential for the subsequent use of the droplets within the library forthe various biological and chemical assays described herein.

The droplets comprised within the emulsion libraries of the presentinvention are contained within an immiscible fluorocarbon oil comprisingat least one fluorosurfactant. In some embodiments, the fluorosurfactantcomprised within immiscible fluorocarbon oil is a block copolymerconsisting of one or more perfluorinated polyether (PFPE) blocks and oneor more polyethylene glycol (PEG) blocks. In other embodiments, thefluorosurfactant is a triblock copolymer consisting of a PEG centerblock covalently bound to two PFPE blocks by amide linking groups. Thepresence of the fluorosurfactant (similar to uniform size of thedroplets in the library) is critical to maintain the stability andintegrity of the droplets and is also essential for the subsequent useof the droplets within the library for the various biological andchemical assays described herein. Fluids (e.g., aqueous fluids,immiscible oils, etc.) and other surfactants that can be utilized in thedroplet libraries of the present invention are described in greaterdetail herein.

The droplet libraries of the present invention are very stable and arecapable of long-term storage. The droplet libraries are determined to bestable if the droplets comprised within the libraries maintain theirstructural integrity, that is the droplets do not rupture and elementsdo not diffuse from the droplets. The droplets libraries are alsodetermined to be stable if the droplets comprised within the librariesdo not coalesce spontaneously (without additional energy input, such aselectrical fields described in detail herein). Stability can be measuredat any temperature. For example, the droplets are very stable and arecapable of long-term storage at any temperature; for example, e.g., −70°C., 0° C., 4° C., 37° C., room temperature, 75° C. and 95° C.Specifically, the droplet libraries of the present invention are stablefor at least 30 days. More preferably, the droplets are stable for atleast 60 days. Most preferably, the droplets are stable for at least 90days.

The present invention provides an emulsion library comprising aplurality of aqueous droplets within an immiscible fluorocarbon oilcomprising at least one fluorosurfactant, wherein each droplet isuniform in size and comprises the same aqueous fluid and comprises adifferent library element. The present invention also provides a methodfor forming the emulsion library comprising providing a single aqueousfluid comprising different library elements, encapsulating each libraryelement into an aqueous droplet within an immiscible fluorocarbon oilcomprising at least one fluorosurfactant, wherein each droplet isuniform in size and comprises the same aqueous fluid and comprises adifferent library element, and pooling the aqueous droplets within animmiscible fluorocarbon oil comprising at least one fluorosurfactant,thereby forming an emulsion library.

For example, in one type of emulsion library, all different types ofelements (e.g., cells or beads), are pooled in a single source containedin the same medium. After the initial pooling, the cells or beads arethen encapsulated in droplets to generate a library of droplets whereineach droplet with a different type of bead or cell is a differentlibrary element. The dilution of the initial solution enables theencapsulation process. In some embodiments, the droplets formed willeither contain a single cell or bead or will not contain anything, i.e.,be empty. In other embodiments, the droplets formed will containmultiple copies of a library element. The cells or beads beingencapsulated are generally variants on the same type of cell or bead. Inone example, the cells can comprise cancer cells of a tissue biopsy, andeach cell type is encapsulated to be screened for genomic data oragainst different drug therapies. Another example is that 10¹¹ or 10¹⁵different type of bacteria; each having a different plasmid splicedtherein, are encapsulated. One example is a bacterial library where eachlibrary element grows into a clonal population that secretes a varianton an enzyme.

In another example, the emulsion library comprises a plurality ofaqueous droplets within an immiscible fluorocarbon oil, wherein a singlemolecule is encapsulated, such that there is a single molecule containedwithin a droplet for every 20-60 droplets produced (e.g., 20, 25, 30,35, 40, 45, 50, 55, 60 droplets, or any integer in between). Singlemolecules are encapsulated by diluting the solution containing themolecules to such a low concentration that the encapsulation of singlemolecules is enabled. In one specific example, a LacZ plasmid DNA wasencapsulated at a concentration of 20 fM after two hours of incubationsuch that there was about one gene in 40 droplets, where 10 μm dropletswere made at 10 kHz per second. Formation of these libraries rely onlimiting dilutions.

The present invention also provides an emulsion library comprising atleast a first aqueous droplet and at least a second aqueous dropletwithin a fluorocarbon oil comprising at least one fluorosurfactant,wherein the at least first and the at least second droplets are uniformin size and comprise a different aqueous fluid and a different libraryelement. The present invention also provides a method for forming theemulsion library comprising providing at least a first aqueous fluidcomprising at least a first library of elements, providing at least asecond aqueous fluid comprising at least a second library of elements,encapsulating each element of said at least first library into at leasta first aqueous droplet within an immiscible fluorocarbon oil comprisingat least one fluorosurfactant, encapsulating each element of said atleast second library into at least a second aqueous droplet within animmiscible fluorocarbon oil comprising at least one fluorosurfactant,wherein the at least first and the at least second droplets are uniformin size and comprise a different aqueous fluid and a different libraryelement, and pooling the at least first aqueous droplet and the at leastsecond aqueous droplet within an immiscible fluorocarbon oil comprisingat least one fluorosurfactant thereby forming an emulsion library.

For example, in one type of emulsion library, there are library elementsthat have different particles, i.e., cells or beads in a differentmedium and are encapsulated prior to pooling. As exemplified in FIG. 2,a specified number of library of elements, i.e., n number of differentcells or beads, are contained within different mediums. Each of thelibrary elements are separately emulsified and pooled, at which pointeach of the n number of pooled different library elements are combinedand pooled into a single pool. The resultant pool contains a pluralityof water-in-oil emulsion droplets each containing a different type ofparticle.

In some embodiments, the droplets formed will either contain a singlelibrary element or will not contain anything, i.e., be empty. In otherembodiments, the droplets formed will contain multiple copies of alibrary element. The contents of the beads follow a Poissondistribution, where there is a discrete probability distribution thatexpresses the probability of a number of events occurring in a fixedperiod of time if these events occur with a known average rate andindependently of the time since the last event. The oils and surfactantsused to create the libraries prevents the exchange of the contents ofthe library between droplets.

Examples of assays that utilize these emulsion libraries are ELISAassays. The present invention provides another emulsion librarycomprising a plurality of aqueous droplets within an immisciblefluorocarbon oil comprising at least one fluorosurfactant, wherein eachdroplet is uniform in size and comprises at least a first antibody, anda single element linked to at least a second antibody, wherein saidfirst and second antibodies are different. In one example, each libraryelement comprises a different bead, wherein each bead is attached to anumber of antibodies and the bead is encapsulated within a droplet thatcontains a different antibody in solution. These antibodies can then beallowed to form “ELISA sandwiches,” which can be washed and prepared fora ELISA assay. Further, these contents of the droplets can be altered tobe specific for the antibody contained therein to maximize the resultsof the assay. A specific example of an ELSA assay is shown in Example 5and in FIG. 3.

The present invention also provides another emulsion library comprisinga plurality of aqueous droplets within an immiscible fluorocarbon oilcomprising at least one fluorosurfactant, wherein each droplet isuniform in size and comprises at least a first element linked to atleast a first antibody, and at least a second element linked to at leasta second antibody, wherein said first and second antibodies aredifferent. In one example of a Protein-Fragment Complementation Assay(PCA), library droplets are prepared to contain a mixture of twodifferent antibodies. Wherein the two antibodies bind with strongaffinity to different epitopes of the antigen molecule that is to bedetected. Detection is achieved by tethering protein fragments to theeach of the antibodies such that when held in proximity the twofragments create an active enzyme capable of turning over a fluorogenicsubstrate, only in the presence of the antigen. For example, as shown inFIG. 4 Panel A, the cell is not secreting any antigen hence thefluorogenic substrate is not converted into a fluorescent product. Bycontrast, in Panel B, the cell is secreting the antigen. Hence when theantibodies bind to it the two protein fragments are held in close enoughproximity to form an active enzyme. The intensity of the fluorescencesignal generated from these sandwiches is indicative of the antigenconcentration in the droplet.

In another example, of the emulsion library, the library begins with acertain number of library elements, which may contain proteins, enzymes,small molecules and PCR primers, among other reagents. However, there isno Poisson distribution in these droplet libraries, Rather, each libraryis added to a droplet in a specific concentration. In these dropletlibraries, there are a large number of the reagent contained within thedroplets. With small molecule chemical compounds, each library elementcan be the same small molecule chemical compound at differentconcentrations or be completely different small molecule chemicalcompound per element. When encapsulating PCR primers there are anynumber of a single type of primer pairs contained within each droplet.

Labels can be used for identification of the library elements of thevarious types of droplet libraries. Libraries can be labeled for uniqueidentification of each library element by any means known in the art.The label can be an optical label, an enzymatic label or a radioactivelabel. The label can be any detectable label, e.g., a protein, a DNAtag, a dye, a quantum dot or a radio frequency identification tag, orcombinations thereof. Preferably the label is an optical label. Thelabel can be detected by any means known in the art. Preferably, thelabel is detected by fluorescence polarization, fluorescence intensity,fluorescence lifetime, fluorescence energy transfer, pH, ionic content,temperature or combinations thereof. Various labels and means fordetection are described in greater detail herein.

Specifically, after a label is added to each of the various libraryelements, the elements are then encapsulated and each of the dropletscontains a unique label so that the library elements may be identified.In one example, by using various combinations of labels and detectionmethods, it is possible to use two different colors with differentintensities or to use a single color at a different intensity anddifferent florescence anisotropy.

Optical labels are also utilized in quality control in order to ensurethat the droplet libraries are well controlled, and that equal number ofeach library elements are contained within uniform volumes in eachdroplet library. After 120 minutes of mixing, using 8-labels in a96-member library, the average number of droplets is 13,883 for each ofthe library elements. As Table 1 shows below, there is very littlevariation between the number of droplets for each library element, i.e.,between −0.8% to +1.1%. The slight variation in the number of dropletsallows the pooled droplet libraries to be used in any number of assays.

TABLE 1 Element G1 G2 G3 G4 G5 G6 G7 G8 # drops 13913 13898 14036 1389813834 13927 13788 13769 % variation +0.2% 0% +1.1% 0% −0.4% +0.3% −0.7%−0.8%

In some quality control examples, 384-member libraries were preparedwith eight optical labels; typically 5 to 20 micro-liters of eachlibrary element are emulsified into approximately 10 picoliter volumedroplets so there are about 1 million droplets of each library elementand 384 million droplets in the library.

The eight optical labels are a dye at concentrations that increase by afactor of c (where c ranges from about 1.2 to 1.4) from one opticallabel to the next so that the nth optical label has (c)(n−1) the dyeconcentration of the lowest concentration. Optical labels are used withconcentrations between 10 nM and 1 uM. Typically, the range of opticallabel concentrations for one series of labels is 1 order of magnitude(e.g., 10 nM to 100 nM with a multiplier of 1.43 for each increasinglabel concentration). A larger range of droplet label concentrations canalso be used. Further, multiplexed two-color labels can be used as well.

Plates are prepared with 384 separate library elements in separate wellsof the 384-well plates; 8 of which have optical labels. The libraryelements are made into droplets, collected in a vial, (also known as acreaming tower) and the collection is mixed on the mixer for severalhours. The mixer works by flipping the vial over about once every 30seconds and then allowing the droplets to rise. Multiple plates can beemulsified and pooled or collected sequentially into the same vial.

A small fraction of the droplets are taken out of the vial to verify 1)that the droplets are present in the correct predetermined ratio and 2)that the droplets are of uniform size. Typically, 1,000 to 10,000droplets of each library element (0.384 to 3.84 million QC-droplets) areremoved from the vial through a PEEK line in the center opening in thevial cap by positive displacement with a drive oil infused through theside opening in vial cap. The PEEK line takes the droplets into a porton a microfluidic chip at a rate of several thousand droplets/second;for 10 picoliter droplets at a rate of 3000 droplets/s corresponds to atypical infusion rate of roughly 110 micro-liters/hr. Once on chip thedroplets are spaced out by adding oil before they are imaged and passone droplet at a time through a laser excitation spot. Maximumfluorescence intensity data from individual droplets is collected forall of the QC-droplets and histograms are built to show the number ofdroplets within a given fluorescence intensity range. As expected, ifeight of the library elements have optical labels, then there are eightpeaks in the histograms. The increasing concentration factor c=1.38results in uniformly separated peaks across one decade when plotted on alog scale. The relative number of droplets in each peak is used as aquality metric to validate that the libraries were prepared with theexpected relative representation. In this example, the percent variationis determined to be only 2.7% demonstrating that all library elementshave uniform representation.

Image analysis can be utilized to determine and monitor osmotic pressurewithin the droplets. Osmotic pressure (e.g., two member library preparedwith a small difference in buffer concentration) can effect droplets.Specifically, droplets with a lower salt concentration shrink over timeand droplets with higher salt concentration grow over time, untiluniform salt concentrations are achieved. Thus it.

Image analysis can also be utilizes for quality control of the libraryreformatting process. After the various library elements are generated,pooled and mixed, optical labels can be used to verify uniformrepresentation of all library elements. Additionally, image analysis isused to verify uniform volume for all droplets.

Further, image analysis can be used for shelf life testing byquantifying the materials performance. Droplets are stored in vialsunder a variety of conditions to test droplets stability againstdroplet-droplet coalescence events. Conditions tested includetemperature, vibration, presence of air in vials, surfactant type, andsurfactant concentration. A Quality Score of percent coalescence iscalculated by image analysis. Shelf-life for the droplet libraries ofthe present invention exceed 90 days.

Microfluidic Systems

Reagents can be reformatted as droplet libraries utilizing automateddevices. Specifically, the library elements can be placed onto platescontaining any number of wells, i.e. 96, 384, etc. The plates can thenbe placed in an Automated Droplet Library Production machine (or othersuch automated device known in the art), which forms the droplets andputs them into a vial or other such container, containing the ready touse droplet library. In general, the process aspirates each of thelibrary elements from the well plates through tubing connected to amicrofluidic device (described in greater detail herein) which can beused to form the droplets. The tubing that aspirates the libraryelements can be rinsed at a wash station and then the process can berepeated for the next library element.

A collection vial can be used to contain the droplets made using theAutomated Droplet Library Production. In one example, the collectionvial has two holes, a first hole in the center of the vial cap and asecond hole part way to the edge of the vial cap. The vial is firstfilled with oil through the second hole to purge air out first hole, theemulsion is then introduced to the vial through the first hole,typically this is done sequentially one library element at a time at lowvolume fraction, and oil is displaced and goes out through the secondhole. The collected droplets can be stored in the vial for periods oftime in excess of 3 months. To remove the emulsion for use or to makesmaller aliquots, oil is introduced through the second opening todisplace the emulsion and drive out the first opening.

The droplet libraries of the present invention are preferably formed byutilizing microfluidic devices and are preferably utilized to performvarious biological and chemical assays on microfluidic devices, asdescribed in detail herein. The present invention also provides embeddedmicrofluidic nozzles. In order to create a monodisperse (<1.5%polydispersity) emulsion directly from a library well, a nozzle can beformed directly into the fitting used to connect the storagewell/reservoir (e.g. syringe) to a syringe tip (e.g. capillary tubing).Examples of suitable nozzles to create the droplet libraries of theinstant invention are described in WO 2007/081385 and WO 2008/063227.

Since the flow is three dimensional, under this design surface wettingeffects are minimized. The nozzle can be made from one or two oil linesproviding constant flow of oil into the nozzle, a connection to thecapillary tubing, and a connection to the storage well/reservoir (e.g.syringe). The high resolution part of the nozzle can be made out of asmall bore tubing or a small, simple part molded or stamped from anappropriate material (TEFLON, plastic, metal, etc). If necessary, thenozzle itself could be formed into the tip of the ferrule using postmold processing such as laser ablation or drilling.

This nozzle design eliminates the surface wetting issues surrounding thequasi-2D flow associated with typical microfluidic nozzles made usingsoft lithography or other standard microfluidic chip manufacturingtechniques. This is because the nozzle design is fully 3-dimensional,resulting is a complete isolation of the nozzle section from thecontinuous aqueous phase. This same design can also be used forgeneration of emulsions required for immediate use, where the aqueousline would be attached directly to a syringe and the outlet of thenozzle would be used to transport the emulsion to the point of use (e.g.into a microfluidic PCR chip, delay line, etc).

In another embodiment, the present invention provides compositions andmethods to directly emulsify library elements from standard librarystorage geometries (e.g. 96 well plates, etc). In order to create amonodisperse emulsion from fluids contained in a library well plate,this invention would include microfluidic based nozzles manufacturedsimultaneously with an appropriately designed fluidic interconnect orwell.

Specifically, the microfluidic devices and methods described herein arebased on the creation and electrical manipulation of aqueous phasedroplets (e.g., droplet libraries) completely encapsulated by an inertimmiscible oil stream. This combination enables precise dropletgeneration, highly efficient, electrically addressable, dropletcoalescence, and controllable, electrically addressable single dropletsorting. The microfluidic devices include one or more channels andmodules. A schematic illustrating one example of interacting modules ofa microfluidic substrate is shown in FIG. 1. The integration of thesemodules is an essential enabling technology for a droplet based,high-throughput microfluidic reactor system and provides an ideal systemfor utilizing the droplet libraries provided herein for numerousbiological, chemical, or diagnostic applications.

Substrates

The microfluidic device of the present invention includes one or moreanalysis units. An “analysis unit” is a microsubstrate, e.g., amicrochip. The terms microsubstrate, substrate, microchip, and chip areused interchangeably herein. The analysis unit includes at least oneinlet channel, at least one main channel and at least one inlet module.The analysis unit can further include at least one coalescence module.at least one detection module and one or more sorting modules. Thesorting module can be in fluid communication with branch channels whichare in fluid communication with one or more outlet modules (collectionmodule or waste module). For sorting applications, at least onedetection module cooperates with at least one sorting module to divertflow via a detector-originated signal. It shall be appreciated that the“modules” and “channels” are in fluid communication with each other andtherefore may overlap; i.e., there may be no clear boundary where amodule or channel begins or ends. A plurality of analysis units of theinvention may be combined in one device. The dimensions of the substrateare those of typical microchips, ranging between about 0.5 cm to about15 cm per side and about 1 micron to about 1 cm in thickness. Theanalysis unit and specific modules are described in further detail in WO2006/040551; WO 2006/040554; WO 2004/002627; WO 2004/091763; WO2005/021151; WO 2006/096571; WO 2007/089541; WO 2007/081385 and WO2008/063227. A variety of materials and methods can be used to form anyof the described components of the systems and devices of the invention.For example, various components of the invention can be formed fromsolid materials, in which the channels can be formed via molding,micromachining, film deposition processes such as spin coating andchemical vapor deposition, laser fabrication, photolithographictechniques, etching methods including wet chemical or plasma processes,and the like. See, for example, Angell, et al., Scientific American,248:44-55, 1983. At least a portion of the fluidic system can be formedof silicone by molding a silicone chip. Technologies for precise andefficient formation of various fluidic systems and devices of theinvention from silicone are known. Various components of the systems anddevices of the invention can also be formed of a polymer, for example,an elastomeric polymer such as polydimethylsiloxane (“PDMS”),polytetrafluoroethylene (“PTFE”) or TEFLON, or the like.

Silicone polymers are preferred, for example, the silicone elastomerpolydimethylsiloxane. Non-limiting examples of PDMS polymers includethose sold under the trademark Sylgard by Dow Chemical Co., Midland,Mich., and particularly Sylgard 182, Sylgard 184, and Sylgard 186.Silicone polymers including PDMS have several beneficial propertiessimplifying formation of the microfluidic structures of the invention.For instance, such materials are inexpensive, readily available, and canbe solidified from a prepolymeric liquid via curing with heat. Forexample, PDMSs are typically curable by exposure of the prepolymericliquid to temperatures of about, for example, about 65° C. to about 75°C. for exposure times of, for example, about an hour. Also, siliconepolymers, such as PDMS, can be elastomeric and thus may be useful forforming very small features with relatively high aspect ratios,necessary in certain embodiments of the invention. Flexible (e.g.,elastomeric) molds or masters can be advantageous in this regard.

One advantage of forming structures such as microfluidic structures ofthe invention from silicone polymers, such as PDMS, is the ability ofsuch polymers to be oxidized, for example by exposure to anoxygen-containing plasma such as an air plasma, so that the oxidizedstructures contain, at their surface, chemical groups capable ofcross-linking to other oxidized silicone polymer surfaces or to theoxidized surfaces of a variety of other polymeric and non-polymericmaterials. Thus, components can be formed and then oxidized andessentially irreversibly sealed to other silicone polymer surfaces, orto the surfaces of other substrates reactive with the oxidized siliconepolymer surfaces, without the need for separate adhesives or othersealing means. In most cases, sealing can be completed simply bycontacting an oxidized silicone surface to another surface without theneed to apply auxiliary pressure to form the seal. That is, thepre-oxidized silicone surface acts as a contact adhesive againstsuitable mating surfaces. Specifically, in addition to beingirreversibly sealable to itself, oxidized silicone such as oxidized PDMScan also be sealed irreversibly to a range of oxidized materials otherthan itself including, for example, glass, silicon, silicon oxide,quartz, silicon nitride, polyethylene, polystyrene, glassy carbon, andepoxy polymers, which have been oxidized in a similar fashion to thePDMS surface (for example, via exposure to an oxygen-containing plasma).Oxidation and sealing methods useful in the context of the presentinvention, as well as overall molding techniques, are described in theart, for example, in Duffy et al., “Rapid Prototyping of MicrofluidicSystems and Polydimethylsiloxane,” Anal. Chem., 70:474-480, 1998.

Another advantage to forming microfluidic structures of the invention(or interior, fluid-contacting surfaces) from oxidized silicone polymersis that these surfaces can be much more hydrophilic than the surfaces oftypical elastomeric polymers (where a hydrophilic interior surface isdesired). Such hydrophilic channel surfaces can thus be more easilyfilled and wetted with aqueous solutions than can structures comprisedof typical, unoxidized elastomeric polymers or other hydrophobicmaterials.

Channels

The microfluidic substrates of the present invention include channelsthat form the boundary for a fluid. A “channel,” as used herein, means afeature on or in a substrate that at least partially directs the flow ofa fluid. In some cases, the channel may be formed, at least in part, bya single component, e.g., an etched substrate or molded unit. Thechannel can have any cross-sectional shape, for example, circular, oval,triangular, irregular, square or rectangular (having any aspect ratio),or the like, and can be covered or uncovered (i.e., open to the externalenvironment surrounding the channel). In embodiments where the channelis completely covered, at least one portion of the channel can have across-section that is completely enclosed, and/or the entire channel maybe completely enclosed along its entire length with the exception of itsinlet and outlet.

The channels of the invention can be formed, for example by etching asilicon chip using conventional photolithography techniques, or using amicromachining technology called “soft lithography” as described byWhitesides and Xia, Angewandte Chemie International Edition 37, 550(1998).

An open channel generally will include characteristics that facilitatecontrol over fluid transport, e.g., structural characteristics (anelongated indentation) and/or physical or chemical characteristics(hydrophobicity vs. hydrophilicity) and/or other characteristics thatcan exert a force (e.g., a containing force) on a fluid. The fluidwithin the channel may partially or completely fill the channel. In somecases the fluid may be held or confined within the channel or a portionof the channel in some fashion, for example, using surface tension(e.g., such that the fluid is held within the channel within a meniscus,such as a concave or convex meniscus). In an article or substrate, some(or all) of the channels may be of a particular size or less, forexample, having a largest dimension perpendicular to fluid flow of lessthan about 5 mm, less than about 2 mm, less than about 1 mm, less thanabout 500 microns, less than about 200 microns, less than about 100microns, less than about 60 microns, less than about 50 microns, lessthan about 40 microns, less than about 30 microns, less than about 25microns, less than about 10 microns, less than about 3 microns, lessthan about 1 micron, less than about 300 nm, less than about 100 nm,less than about 30 nm, or less than about 10 nm or less in some cases.

A “main channel” is a channel of the device of the invention whichpermits the flow of molecules, cells, small molecules or particles pasta coalescence module for coalescing one or more droplets, and, ifpresent, a detection module for detection (identification) ormeasurement of a droplet and a sorting module for sorting a dropletbased on the detection in the detection module. The main channel istypically in fluid communication with the coalescence, detection and/orsorting modules, as well as, an inlet channel of the inlet module. Themain channel is also typically in fluid communication with an outletmodule and optionally with branch channels, each of which may have acollection module or waste module. These channels permit the flow ofmolecules, cells, small molecules or particles out of the main channel.An “inlet channel” permits the flow of molecules, cells, small moleculesor particles into the main channel. One or more inlet channelscommunicate with one or more means for introducing a sample into thedevice of the present invention. The inlet channel communicates with themain channel at an inlet module.

The microfluidic substrate can also comprise one or more fluid channelsto inject or remove fluid in between droplets in a droplet stream forthe purpose of changing the spacing between droplets.

The channels of the device of the present invention can be of anygeometry as described. However, the channels of the device can comprisea specific geometry such that the contents of the channel aremanipulated, e.g., sorted, mixed, prevent clogging, etc.

A microfluidic substrate can also include a specific geometry designedin such a manner as to prevent the aggregation of biological/chemicalmaterial and keep the biological/chemical material separated from eachother prior to encapsulation in droplets. The geometry of channeldimension can be changed to disturb the aggregates and break them apartby various methods, that can include, but is not limited to, geometricpinching (to force cells through a (or a series of) narrow region(s),whose dimension is smaller or comparable to the dimension of a singlecell) or a barricade (place a series of barricades on the way of themoving cells to disturb the movement and break up the aggregates ofcells).

To prevent material (e.g., cells and other particles or molecules) fromadhering to the sides of the channels, the channels (and coverslip, ifused) may have a coating which minimizes adhesion. The surface of thechannels of the microfluidic device can be coated with any anti-wettingor blocking agent for the dispersed phase. The channel can be coatedwith any protein to prevent adhesion of the biological/chemical sample.Channels can be coated by any means known in the art. For example, thechannels are coated with TEFLON, BSA, PEG-silane and/or fluorosilane inan amount sufficient to prevent attachment and prevent clogging. Inanother example, the channels can be coated with a cyclized transparentoptical polymer obtained by copolymerization of perfluoro (alkenyl vinylethers), such as the type sold by Asahi Glass Co. under the trademarkCytop. In such an example, the coating is applied from a 0.1-0.5 wt %solution of Cytop CTL-809M in CT-Solv 180. This solution can be injectedinto the channels of a microfluidic device via a plastic syringe. Thedevice can then be heated to about 90° C. for 2 hours, followed byheating at 200° C. for an additional 2 hours. In another embodiment, thechannels can be coated with a hydrophobic coating of the type sold byPPG Industries, Inc. under the trademark Aquapel (e.g.,perfluoroalkylalkylsilane surface treatment of plastic and coatedplastic substrate surfaces in conjunction with the use of a silicaprimer layer) and disclosed in U.S. Pat. No. 5,523,162. By fluorinatingthe surfaces of the channels, the continuous phase preferentially wetsthe channels and allows for the stable generation and movement ofdroplets through the device. The low surface tension of the channelwalls thereby minimizes the accumulation of channel cloggingparticulates.

The surface of the channels in the microfluidic device can be alsofluorinated by any means known in the art to prevent undesired wettingbehaviors. For example, a microfluidic device can be placed in apolycarbonate dessicator with an open bottle of(tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane. The dessicatoris evacuated for 5 minutes, and then sealed for 20-40 minutes. Thedessicator is then backfilled with air and removed. This approach uses asimple diffusion mechanism to enable facile infiltration of channels ofthe microfluidic device with the fluorosilane and can be readily scaledup for simultaneous device fluorination.

Fluids

The fluids described herein are related to the fluids within the dropletlibraries and to the fluids within a microfluidic device.

The microfluidic device of the present invention is capable ofcontrolling the direction and flow of fluids and entities within thedevice. The term “flow” means any movement of liquid or solid through adevice or in a method of the invention, and encompasses withoutlimitation any fluid stream, and any material moving with, within oragainst the stream, whether or not the material is carried by thestream. For example, the movement of molecules, beads, cells or virionsthrough a device or in a method of the invention, e.g. through channelsof a microfluidic chip of the invention, comprises a flow. This is so,according to the invention, whether or not the molecules, beads, cellsor virions are carried by a stream of fluid also comprising a flow, orwhether the molecules, cells or virions are caused to move by some otherdirect or indirect force or motivation, and whether or not the nature ofany motivating force is known or understood. The application of anyforce may be used to provide a flow, including without limitation,pressure, capillary action, electro-osmosis, electrophoresis,dielectrophoresis, optical tweezers, and combinations thereof, withoutregard for any particular theory or mechanism of action, so long asmolecules, cells or virions are directed for detection, measurement orsorting according to the invention. Specific flow forces are describedin further detail herein.

The flow stream in the main channel is typically, but not necessarily,continuous and may be stopped and started, reversed or changed in speed.A liquid that does not contain sample molecules, cells or particles canbe introduced into a sample inlet well or channel and directed throughthe inlet module, e.g., by capillary action, to hydrate and prepare thedevice for use. Likewise, buffer or oil can also be introduced into amain inlet region that communicates directly with the main channel topurge the device (e.g., or “dead” air) and prepare it for use. Ifdesired, the pressure can be adjusted or equalized, for example, byadding buffer or oil to an outlet module.

As used herein, the term “fluid stream” or “fluidic stream” refers tothe flow of a fluid, typically generally in a specific direction. Thefluidic stream may be continuous and/or discontinuous. A “continuous”fluidic stream is a fluidic stream that is produced as a single entity,e. g., if a continuous fluidic stream is produced from a channel, thefluidic stream, after production, appears to be contiguous with thechannel outlet. The continuous fluidic stream is also referred to as acontinuous phase fluid or carrier fluid. The continuous fluidic streammay be laminar, or turbulent in some cases.

Similarly, a “discontinuous” fluidic stream is a fluidic stream that isnot produced as a single entity. The discontinuous fluidic stream isalso referred to as the dispersed phase fluid or sample fluid. Adiscontinuous fluidic stream may have the appearance of individualdroplets, optionally surrounded by a second fluid. The dispersed phasefluid can include a biological/chemical material. Thebiological/chemical material can be tissues, cells, particles, proteins,antibodies, amino acids, nucleotides, small molecules, andpharmaceuticals. The biological/chemical material can include one ormore labels known in the art. The label can be an optical label, anenzymatic label or a radioactive label. The label can be any detectablelabel, e.g., a protein, a DNA tag, a dye, a quantum dot or a radiofrequency identification tag, or combinations thereof. Preferably thelabel is an optical label. The label can be detected by any means knownin the art. Preferably, the label is detected by fluorescencepolarization, fluorescence intensity, fluorescence lifetime,fluorescence energy transfer, pH, ionic content, temperature orcombinations thereof. Various labels and means for detection aredescribed in greater detail herein.

The term “emulsion” refers to a preparation of one liquid distributed insmall globules (also referred to herein as drops, droplets orNanoReactors) in the body of a second liquid. The first and secondfluids are immiscible with each other. For example, the discontinuousphase can be an aqueous solution and the continuous phase can ahydrophobic fluid such as an oil. This is termed a water in oilemulsion. Alternatively, the emulsion may be a oil in water emulsion. Inthat example, the first liquid, which is dispersed in globules, isreferred to as the discontinuous phase, whereas the second liquid isreferred to as the continuous phase or the dispersion medium. Thecontinuous phase can be an aqueous solution and the discontinuous phaseis a hydrophobic fluid, such as an oil (e.g., decane, tetradecane, orhexadecane). The droplets or globules of oil in an oil in water emulsionare also referred to herein as “micelles”, whereas globules of water ina water in oil emulsion may be referred to as “reverse micelles”.

The fluidic droplets may each be substantially the same shape and/orsize. The droplets may be uniform in size. The shape and/or size can bedetermined, for example, by measuring the average diameter or othercharacteristic dimension of the droplets. The “average diameter” of aplurality or series of droplets is the arithmetic average of the averagediameters of each of the droplets. Those of ordinary skill in the artwill be able to determine the average diameter (or other characteristicdimension) of a plurality or series of droplets, for example, usinglaser light scattering, microscopic examination, or other knowntechniques. The diameter of a droplet, in a non-spherical droplet, isthe mathematically-defined average diameter of the droplet, integratedacross the entire surface. The average diameter of a droplet (and/or ofa plurality or series of droplets) may be, for example, less than about1 mm, less than about 500 micrometers, less than about 200 micrometers,less than about 100 micrometers, less than about 75 micrometers, lessthan about 50 micrometers, less than about 25 micrometers, less thanabout 10 micrometers, or less than about 5 micrometers in some cases.The average diameter may also be at least about 1 micrometer, at leastabout 2 micrometers, at least about 3 micrometers, at least about 5micrometers, at least about 10 micrometers, at least about 15micrometers, or at least about 20 micrometers in certain cases.

As used herein, the term “NanoReactor” and its plural encompass theterms “droplet”, “nanodrop”, “nanodroplet”, “microdrop” or“microdroplet” as defined herein, as well as an integrated system forthe manipulation and probing of droplets, as described in detail herein.Nanoreactors as described herein can be 0.1-1000 μm (e.g., 0.1, 0.2 . .. 5, 10, 15, 20, 25, 30, 35, 40, 45, 50 . . . 1000), or any size withinthis range. Droplets at these dimensions tend to conform to the size andshape of the channels, while maintaining their respective volumes. Thus,as droplets move from a wider channel to a narrower channel they becomelonger and thinner, and vice versa.

The microfluidic substrate of this invention most preferably generateround, highly uniform, monodisperse droplets (<1.5% polydispersity).Droplets and methods of forming monodisperse droplets in microfluidicchannels is described in WO 2006/040551; WO 2006/040554; WO 2004/002627;WO 2004/091763; WO 2005/021151; WO 2006/096571; WO 2007/089541; WO2007/081385 and WO 2008/063227.

The droplet forming liquid is typically an aqueous buffer solution, suchas ultrapure water (e.g., 18 mega-ohm resistivity, obtained, for exampleby column chromatography), 10 mM Tris HCl and 1 mM EDTA (TE) buffer,phosphate buffer saline (PBS) or acetate buffer. Any liquid or bufferthat is physiologically compatible with the population of molecules,cells or particles to be analyzed and/or sorted can be used. The fluidpassing through the main channel and in which the droplets are formed isone that is immiscible with the droplet forming fluid. The fluid passingthrough the main channel can be a non-polar solvent, decane (e.g.,tetradecane or hexadecane), fluorocarbon oil, silicone oil or anotheroil (for example, mineral oil).

The droplet may also contain biological/chemical material (e.g.,molecules, cells, or other particles) for combination, analysis and/orsorting in the device. The droplets of the dispersed phase fluid cancontain more than one particle or can contain no more than one particle.

Droplets of a sample fluid can be formed within the inlet module on themicrofluidic device or droplets (or droplet libraries) can be formedbefore the sample fluid is introduced to the microfluidic device (“offchip” droplet formation). To permit effective interdigitation,coalescence and detection, the droplets comprising each sample to beanalyzed must be monodisperse. As described in more detail herein, inmany applications, different samples to be analyzed are contained withindroplets of different sizes. Droplet size must be highly controlled toensure that droplets containing the correct contents for analysis andcoalesced properly. As such, the present invention provides devices andmethods for forming droplets and droplet libraries.

Surfactants

The fluids used in the invention may contain one or more additives, suchas agents which reduce surface tensions (surfactants). Surfactants caninclude Tween, Span, fluorosurfactants, and other agents that aresoluble in oil relative to water. In some applications, performance isimproved by adding a second surfactant to the aqueous phase. Surfactantscan aid in controlling or optimizing droplet size, flow and uniformity,for example by reducing the shear force needed to extrude or injectdroplets into an intersecting channel. This can affect droplet volumeand periodicity, or the rate or frequency at which droplets break offinto an intersecting channel. Furthermore, the surfactant can serve tostabilize aqueous emulsions in fluorinated oils from coalescing. Thepresent invention provides compositions and methods to stabilize aqueousdroplets in a fluorinated oil and minimize the transport of positivelycharged reagents (particularly, fluorescent dyes) from the aqueous phaseto the oil phase.

The droplets may be coated with a surfactant. Preferred surfactants thatmay be added to the continuous phase fluid include, but are not limitedto, surfactants such as sorbitan-based carboxylic acid esters (e.g., the“Span” surfactants, Fluka Chemika), including sorbitan monolaurate (Span20), sorbitan monopalmitate (Span 40), sorbitan monostearate (Span 60)and sorbitan monooleate (Span 80), and perfluorinated polyethers (e.g.,DuPont Krytox 157 FSL, FSM, and/or FSH). Other non-limiting examples ofnon-ionic surfactants which may be used include polyoxyethylenatedalkylphenols (for example, nonyl-, p-dodecyl-, and dinonylphenols),polyoxyethylenated straight chain alcohols, polyoxyethylenatedpolyoxypropylene glycols, polyoxyethylenated mercaptans, long chaincarboxylic acid esters (for example, glyceryl and polyglyceryl esters ofnatural fatty acids, propylene glycol, sorbitol, polyoxyethylenatedsorbitol esters, polyoxyethylene glycol esters, etc.) and alkanolamines(e.g., diethanolamine-fatty acid condensates and isopropanolamine-fattyacid condensates). In addition, ionic surfactants such as sodium dodecylsulfate (SDS) may also be used. However, such surfactants are generallyless preferably for many embodiments of the invention. For instance, inthose embodiments where aqueous droplets are used as nanoreactors forchemical reactions (including biochemical reactions) or are used toanalyze and/or sort biomaterials, a water soluble surfactant such as SDSmay denature or inactivate the contents of the droplet.

The carrier fluid can be an oil (e.g., decane, tetradecane orhexadecane) or fluorocarbon oil that contains a surfactant (e.g., anon-ionic surfactant such as a Span surfactant) as an additive(preferably between about 0.2 and 5% by volume, more preferably about2%). A user can preferably cause the carrier fluid to flow throughchannels of the microfluidic device so that the surfactant in thecarrier fluid coats the channel walls.

Fluorocarbon oil continuous phases are well-suited as the continuousphase for aqueous droplet libraries for a number of reasons. Fluorousoils are both hydrophobic and lipophobic. Therefore, they have lowsolubility for components of the aqueous phase and they limit moleculardiffusion between droplets. Also, fluorous oils present an inertinterface for chemistry and biology within droplets. In contrast tohydrocarbon or silicone oils, fluorous oils do not swell PDMS materials,which is a convenient material for constructing microfluidic channels.Finally, fluorocarbon oils have good solubility for gases, which isnecessary for the viability of encapsulated cells.

Combinations of surfactant(s) and oils must be developed to facilitategeneration, storage, and manipulation of droplets to maintain the uniquechemical/biochemical/biological environment within each droplet of adiverse library. Therefore, the surfactant and oil combination must (1)stabilize droplets against uncontrolled coalescence during the dropforming process and subsequent collection and storage, (2) minimizetransport of any droplet contents to the oil phase and/or betweendroplets, and (3) maintain chemical and biological inertness withcontents of each droplet (e.g., no adsorption or reaction ofencapsulated contents at the oil-water interface, and no adverse effectson biological or chemical constituents in the droplets). In addition tothe requirements on the droplet library function and stability, thesurfactant-in-oil solution must be coupled with the fluid physics andmaterials associated with the platform. Specifically, the oil solutionmust not swell, dissolve, or degrade the materials used to construct themicrofluidic chip, and the physical properties of the oil (e.g.,viscosity, boiling point, etc.) must be suited for the flow andoperating conditions of the platform.

Droplets formed in oil without surfactant are not stable to permitcoalescence, so surfactants must be dissolved in the fluorous oil thatis used as the continuous phase for the emulsion library. Surfactantmolecules are amphiphilic—part of the molecule is oil soluble, and partof the molecule is water soluble. When a water-oil interface is formedat the nozzle of a microfluidic chip for example in the inlet moduledescribed herein, surfactant molecules that are dissolved in the oilphase adsorb to the interface. The hydrophilic portion of the moleculeresides inside the droplet and the fluorophilic portion of the moleculedecorates the exterior of the droplet. The surface tension of a dropletis reduced when the interface is populated with surfactant, so thestability of an emulsion is improved. In addition to stabilizing thedroplets against coalescence, the surfactant should be inert to thecontents of each droplet and the surfactant should not promote transportof encapsulated components to the oil or other droplets.

A very large body of fundamental research and commercial applicationdevelopment exists for non-fluorous surfactants and emulsions rangingfrom sub-micron droplets to very large, macroscopic emulsions. Incontrast, fundamental knowledge and commercial practice with fluorinatedoils and surfactants is much less common. More specifically, testing anddevelopment of fluorosurfactants and fluorous oil formulations for theapplication of creating large libraries of micron-scale droplets withunique composition is limited to only a few groups throughout the world.Only a few commercially-available fluorosurfactants that stabilizewater-in-fluorocarbon oil emulsions exist. For instance, surfactantswith short fluorotelomer-tails (typically perfluorinated C₆ to C₁₀) areavailable, but they do not provide sufficient long-term emulsionstability. Fluorosurfactants with longer fluorocarbon tails, such asperfluoropolyether (PFPE), are limited to molecules with ionicheadgroups.

Classes of oils are available from wide variety of fluorinated oils andare available from commercial sources. The requirements for the oil are(1) immiscibility with the aqueous phase, (2) solubility of emulsionstabilizing surfactants in the oil, and (3) compatibility and/orinsolubility of reagents from the droplet phase. Oils includehydrofluoroethers, which are fluorinated alkyl chains coupled withhydrocarbon chemistry through and ether bond. One supplier of this typeof oil is 3M. The products are marketed as Novec Engineered Fluids orHFE-series oils. This oils include but are not limited to, HFE-7500,which is a preferred embodiment as it provides superior dropletstability seems to be higher. Other oils include HFE-7100, −7200, −7600,which are examples of other HFEs available from 3M. These can be used asstand-alone oils or components of oil mixtures to optimize emulsionproperties and performance. Other hydrofluoroethers are also availablefrom other producers, distributors, or resellers may offerhydrofluoroethers.

Another class of oil is perfluoroalkylamines, which are perfluorinatedoils based on perfluoroalkyl amine structures. 3M produces these oils asFluorinert Electronic Liquids (FC-oils). Fluorinert products differ byvariations in alkyl chain length, branch structure, and combinations ofdifferent structures or pure oils. Many of them offer the potential forstand-alone oils or components of oil mixtures to optimize emulsionproperties and performance. Specific examples are Fluorinert FC-3283,Fluorinert FC-40, which are a preferred embodiments. Higher viscosityand boiling point useful for applications requiring elevated temperature(e.g., thermocyling for PCR). Other Fluorinert series can be used forstand-alone oils or components of oil mixtures to optimize emulsionproperties and performance. Again, other perfluoroalkylamines areavailable from other producers, distributors, or resellers may offerperfluoroalkylamines.

Fluorinated organics/solvents offer a number of perfluorinated orpartially fluorinated solvents are available from a variety ofproducers, distributors, and/or resellers. Many of them offer thepotential for stand-alone oils or components of oil mixtures to optimizeemulsion properties and performance. Examples of fluorinated organicreagents utilized, included (but not limited to) trifluoroacetic acidand hexafluoroisopropanol, to improve droplet stability in otherfluorinated oil systems. Additionally, fluoropolymers may also be usedwithin a microfluidic system. Examples of fluoropolymers include, KrytoxGPL oils, Solvay Galden oils, and other liquid fluoropolymers. Otherfluorinated materials find widespread use in a variety of industries,but they are generally not well-known in the disciplines of interfacial,colloidal, physical, or synthetic organic chemistry. Therefore, a numberof other candidates for oils exist in specialty and niche marketapplications. As such, new oils have been targeted partially that areper-fluorinated materials, which are not widely recognized.

The properties of oils selected are based upon their chemicalproperties, such as, among others molecular structure, fluorine contentand solvating strength. Physical properties of oils examined includeviscosity, boiling point, thermal expansion coefficient, oil-in-watersolubility, water-in-oil solubility, dielectric constant, polarity, andoil-in-water surface tension.

Classes of surfactants include fluorosurfactants that can be categorizedby the type of fluorophilic portion of the molecule, the type ofhydrophilic, or polar, portion, and the chemistry used to link thedifferent parts of the molecule. Materials developed are capable ofstabilizing an emulsion or droplet library. The preferred embodiment isthe EA surfactant. Specifically, the EA surfactant is aKrytox-PEG-Krytox. The EA surfactant is a nonionic tri-block copolymersurfactant was developed to avoid issues that the ionic surfactants(e.g., RR, see below) which result from the use of some other ionicsurfactant. Specifically, ionic surfactants interact with chargedspecies in the droplets and can sequester ions (e.g., magnesium requiredfor the PCR reaction) or other reagents to the oil phase. The structureof the EA surfactant comprises a PEG—approximately 600 Da with amine endfunctionality, PFPE—Mn is ˜5000-8000 from a Krytox FSH starting materialand the linker is an amide coupling. Another surfactant includes the RRsurfactant, which is a Krytox ammonium carboxylate.

Alternative materials are alternative fluorophilic portion, i.e., PFPE(Solvay or Demnum), Poly(fluoroalkylacrylate) and other non-polymericand partially fluorinated materials. Alternative head-group chemistryfor the hydrophilic portion includes, non-ionic head groups like PEG(Mw, Mw/Mn (PDI)) and functionality (i.e., diblock, triblock anddendritic). Others include morpholino. Ionic head groups for thehydrophilic portion include anionic, such as elemental and amine saltsand further cationic head portions. Other head group chemistries includezwitterionic, hybrid (e.g., PEG-ionic and zonyl FSO/FSN), lipophilic(e.g, lipophilic to promote bilayer and lipophilic spacer tohydrophile). Another alternative is alternative coupling chemistry suchas, phosphoryl/Friedel-Crafts, spacer to organic handle and others.

Characteristics of surfactants are their molecular structure, determinedby NMR, chromatography (e.g., HPLC, GPC/SEC), FTIR, mass spectrometry,and titrations. Purity of surfactants is another characteristic examinedin addition to the fluorophile-hydrophile balance.

A preferred embodiment includes oil-surfactant formulation for theapplication of library emulsions is R-oil (HFE-7500) mixed with 2 wt %EA surfactant (“REA20”). Concentrations of EA or RR surfactant at 0.1 wt% or lower to 5% or greater. Other formulations of oils and surfactantsand other components added to the aqueous phase are used to improved andoptimized the performance of the droplets performance. Those propertiesof the oil-surfactant mixture include simple mixtures (i.e., one oil andone surfactant, with varied surface concentration), co-surfactants, oilmixtures and additives, such as zonyl and TFA.

Oil and surfactant mixture properties include surfactant solubility,critical micelle concentration (CMC), surfactant diffusivity, andinterfacial tension, i.e., dynamic and equilibrium. Emulsion propertiesare also accounted for, those properties include size (absolute and sizedistribution), stability, transport, and biocompatibility. Stabilityrelates directly to the coalesced droplets and theirdeformability/breaking and shredding ability. More particularly, thestability of the droplets in their generation, storage and shipping.

In general, production of surfactant and oils begins with the synthesisof surfactants and starting materials, such as PEG-diamine, EA and RRand also accounts for the purification processes, characterization,quality control, mixing and packaging.

In one embodiment, the fluorosurfactant can be prepared by reacting theperflourinated polyether DuPont Krytox 157 FSL, FSM, or FSH with aqueousammonium hydroxide in a volatile fluorinated solvent. The solvent andresidual water and ammonia can be removed with a rotary evaporator. Thesurfactant can then be dissolved (e.g., 2.5 wt %) in a fluorinated oil(e.g., Flourinert (3M)), which then serves as the continuous phase ofthe emulsion.

In another embodiment, a quaternary ammonium salt at the terminus of ahydrophilic oligomer is linked to a perfluoropolyether tail as shown inthe following formula:

PFPE-C(O)NH—CH₂CH₂CH₂—(OCH₂CH₂)₃O—CH₂CH₂CH₂—N(CH₃)₃+I-Some specificmolecular features of the present invention include, but are not limitedto, PFPE is from Krytox 157 FSH (Mn-6500), amide bond linking PFPE tohydrophile, propyl group immediately adjacent to the amide, propyl groupimmediately adjacent to the trimethylamino terminus. Specific structuralformations can alter performance relationships, for example, PFPE chainis sufficiently long for molecule to be soluble in perfluorinated oils,amide linker provides hydrolytic stability and hydrogen bonding site,and a combination of PEG and quaternary ammonium cation provide highanchoring strength to the aqueous phase as well as electrostaticrepulsion and steric hindrance to minimize reagent transport.

Variables in the molecular structure include, but are not limited to,PFPE molecular weight and polydispersity, PFPE structure, alternativeperfluorinated tail chemistries, PEG molecular weight andpolydispersity, shorter hydrocarbon linkers (ethyl or methyl versuspropyl), longer hydrocarbon spacers (C4 or higher), alternativecounterions, such as monovalent anions, monovalent, polyatomic anionsand di- or tri-valent counterions (to produce two or more tailfluorosurfactants). Further variables in the molecule structure includealternative linker chemistries (e.g., ether, ester, etc), alternativehydrophilic oligomers (e.g., polyalcohol, polyacrylamide, etc.),alternative quaternary ammonium cations, and alternative ionic groups(e.g., anionic terminus—carboxylate etc.; alternative cations).

The present invention is also directed to the coupling of PEG-diamineswith carboxylic acid-terminated perfluoropolyether (Krytox 157) to formsurfactants. Specifically, the present invention is directed to afluorosurfactant molecule made by the ionic coupling of amine-terminatedpolyethyleneglycol (PEG-amine) with the carboxylic acid of DuPont Krytoxperfluoropolyether (PFPE). The resulting structure conveys goodperformance in the stabilization of aqueous droplets in fluorinated oilin a microfluidic system. Examples of specific surfactants are shown inExamples 1 and 2. Preferred surfactants are also described in WO2008/021123.

The present invention provides droplets with a fluorosurfactantinterface separating the aqueous droplet and its contents from thesurrounding immiscible fluorocarbon oil. In one example, DNAamplification reactions occurring inside these droplets generatematerial that does not interact with the channel walls, and collectionof the DNA-containing droplets for subsequent manipulation andsequencing is straightforward. This technology provides a solution foramplification of DNA from single cells, allowing for both genotyping andwhole genome amplification. In addition, use within a microfluidicdevice or platform as described herein achieves very high throughput,with droplets processed at rates in excess of 5000 droplets per second,enabling greater than 1×10⁶ single-cell droplets to be formed andmanipulated per hour.

Other examples of materials related to this invention include theformation of salts made by combination of various primary, secondary, ortertiary amines with PFPE carboxylic acid. The resulting amphiphilicstructure could be useful as a stand-alone surfactant or a cosurfactant.Similarly, fluorinated materials with carboxylic acids other than KrytoxPFPE could be used to form ionic fluorosurfactants with various aminecontaining compounds.

Alternative amine-containing compounds for use with the presentinvention include, but are not limited to, PEG-monoamine (molecularweights range from 200 to 1,000,000 or more), PEG-diamine (molecularweights range from 200 to 1,000,000 or more), Multifunctional PEG amines(e.g., branched or dendritic structures), other hydrophilic polymersterminated with amines. Sugars include, but are not limited to, Sugars,Peptides, Biomolecules, Ethanolamine or Alkyl amines—primary, secondary,or tertiary (e.g., triethylamine, trimethylamine, methylamine,ethylamine, butylamine)

Alternative fluorinated groups for use with the present inventioninclude, but are not limited to, Krytox FSL and FSM (alternativemolecular weights), Demnum PFPE materials, Fluolink PFPE materials orFluorinated small molecules with carboxylic acids.

The data described herein show that the fluorosurfactants comprised ofPEG amine salts provide better performance (compared to otherfluorosurfactants) for stabilization of aqueous droplets in fluorinatedoils in droplet-based microfluidics applications. These novelsurfactants are useful either in combination with other surfactants oras a stand-alone surfactant system.

Driving Forces

The invention can use pressure drive flow control, e.g., utilizingvalves and pumps, to manipulate the flow of cells, particles, molecules,enzymes or reagents in one or more directions and/or into one or morechannels of a microfluidic device. However, other methods may also beused, alone or in combination with pumps and valves, such aselectro-osmotic flow control, electrophoresis and dielectrophoresis asdescribed in Fulwyer, Science 156, 910 (1974); Li and Harrison,Analytical Chemistry 69, 1564 (1997); Fiedler, et al. AnalyticalChemistry 70, 1909-1915 (1998) and U.S. Pat. No. 5,656,155. Applicationof these techniques according to the invention provides more rapid andaccurate devices and methods for analysis or sorting, for example,because the sorting occurs at or in a sorting module that can be placedat or immediately after a detection module. This provides a shorterdistance for molecules or cells to travel, they can move more rapidlyand with less turbulence, and can more readily be moved, examined, andsorted in single file, i.e., one at a time.

Positive displacement pressure driven flow is a preferred way ofcontrolling fluid flow and dielectrophoresis is a preferred way ofmanipulating droplets within that flow. The pressure at the inlet modulecan also be regulated by adjusting the pressure on the main and sampleinlet channels, for example, with pressurized syringes feeding intothose inlet channels. By controlling the pressure difference between theoil and water sources at the inlet module, the size and periodicity ofthe droplets generated may be regulated. Alternatively, a valve may beplaced at or coincident to either the inlet module or the sample inletchannel connected thereto to control the flow of solution into the inletmodule, thereby controlling the size and periodicity of the droplets.Periodicity and droplet volume may also depend on channel diameter, theviscosity of the fluids, and shear pressure. Examples of drivingpressures and methods of modulating flow are as described in WO2006/040551; WO 2006/040554; WO 2004/002627; WO 2004/091763; WO2005/021151; WO 2006/096571; WO 2007/089541; WO 2007/081385 and WO2008/063227; U.S. Pat. No. 6,540,895 and U.S. Patent ApplicationPublication Nos. 20010029983 and 20050226742

Inlet Module

The microfluidic device of the present invention includes one or moreinlet modules. An “inlet module” is an area of a microfluidic substratedevice that receives molecules, cells, small molecules or particles foradditional coalescence, detection and/or sorting. The inlet module cancontain one or more inlet channels, wells or reservoirs, openings, andother features which facilitate the entry of molecules, cells, smallmolecules or particles into the substrate. A substrate may contain morethan one inlet module if desired. Different sample inlet channels cancommunicate with the main channel at different inlet modules.Alternately, different sample inlet channels can communication with themain channel at the same inlet module. The inlet module is in fluidcommunication with the main channel. The inlet module generallycomprises a junction between the sample inlet channel and the mainchannel such that a solution of a sample (i.e., a fluid containing asample such as molecules, cells, small molecules (organic or inorganic)or particles) is introduced to the main channel and forms a plurality ofdroplets. The sample solution can be pressurized. The sample inletchannel can intersect the main channel such that the sample solution isintroduced into the main channel at an angle perpendicular to a streamof fluid passing through the main channel. For example, the sample inletchannel and main channel intercept at a T-shaped junction; i.e., suchthat the sample inlet channel is perpendicular (90 degrees) to the mainchannel. However, the sample inlet channel can intercept the mainchannel at any angle, and need not introduce the sample fluid to themain channel at an angle that is perpendicular to that flow. The anglebetween intersecting channels is in the range of from about 60 to about120 degrees. Particular exemplary angles are 45, 60, 90, and 120degrees. Embodiments of the invention are also provided in which thereare two or more inlet modules introducing droplets of samples into themain channel. For example, a first inlet module may introduce dropletsof a first sample into a flow of fluid in the main channel and a secondinlet module may introduce droplets of a second sample into the flow offluid in main channel, and so forth. The second inlet module ispreferably downstream from the first inlet module (e.g., about 30 μm).The fluids introduced into the two or more different inlet modules cancomprise the same fluid or the same type of fluid (e.g., differentaqueous solutions). For example, droplets of an aqueous solutioncontaining an enzyme are introduced into the main channel at the firstinlet module and droplets of aqueous solution containing a substrate forthe enzyme are introduced into the main channel at the second inletmodule. Alternatively, the droplets introduced at the different inletmodules may be droplets of different fluids which may be compatible orincompatible. For example, the different droplets may be differentaqueous solutions, or droplets introduced at a first inlet module may bedroplets of one fluid (e.g., an aqueous solution) whereas dropletsintroduced at a second inlet module may be another fluid (e.g., alcoholor oil).

Filters

An important element in making libraries utilizing the microfluidicdevice of the present invention is to include features in the channelsof the device to remove particles that may effect the microfluidicsystem. When emulsions are injected or re-injected onto a microfluidicdevice, they carry contaminants that collect at the nozzle and eitherclog the nozzle and/or induce uncontrolled coalescence up to thecomplete shredding of the emulsion. Debris/contaminants include smalldebris, such as dust or TCS, fibers, goop (glue and/or surfactant) andlarge debris such as PDMS skins/shavings. In one example, the presentinvention provides a post trap for large debris, a pocket trap for smalldebris, a serpentine trap for fibers and a step trap for largedroplets/debris. EAP filters work well to filter out the contaminants.

The filter system filters out these contaminants and most importantlytraps the contaminants out of the main pathway and allow the droplets topass by so the contaminants cannot induce uncontrolled coalescence. Thepresent invention comprises two distinct parts that specifically addresstwo different scales. The first filters contaminants that are largerthan the droplet size. The second filters contaminants that are smallerthan the droplet and nozzle sizes. The large contaminants are easilytrapped but are responsible for inducing uncontrolled coalescence, thesmall contaminants tend to stick to the nozzle and most probably inducewetting that results in the shredding of the emulsion.

To address the issue of large contaminants, a triangular shape filter isused that contains an internal-collection channel and smaller lateralchannels connected to the internal-collection channel with a specificangle. On each side of the triangle are pockets to collect thecontaminants that have been deflected by the triangle and directed thereby the flow of the droplets due to the specific angle of the filter. Inaddition, the collection pockets are connected to a channel of highhydrodynamic resistance so that some of the flow will still go throughand maintain the contaminants in the collection pockets. The lateralcollection channels are located at a stepwise transition between ashallow layer and a deep layer. In one example, the droplets arecollected in the Droplet Collection Channel through the lateral angledchannels. The contaminants are deflected toward the ContaminantCollection Pocket because of the triangular shape and the droplet flow.Because of the use of high resistance channel for the ContaminantsCollection Pockets, the droplets go through them only marginally, butenough to force the trapped contaminants to stay there.

To address the issue of the small contaminants, a series of posts areused, each one being offset by a half-period to the adjacent ones. Thisgeometry intends to create a region of null-recirculation flow at thetip of each post due to the symmetry and contaminants are trapped inthat region. In addition, the posts have an indentation to both increasethe effect of the flow pattern described above and to trap thecontaminants so that they are out of the way of the droplets. The postscan be designed just with an indentation or with a flow-throughrestriction of high hydrodynamic resistance so that the contaminantswill be directed and trapped deep in the structure. The symmetricaldesign creates a region where there is almost no flow, in this regioncreates the conditions to trap the contaminants that are smaller thanthe droplets. The droplets follow the main flow because of the highhydrodynamic resistance conditions. The posts on one side of the channelhave a flow-through to ensure that the contaminants stay trapped there;on the other side the posts have only an indentation. Several series ofthese posts, offset by half of a period are used to increase both thefilter capacity and the odds of trapping any given contaminant.

Droplet Interdigitation

Particular design embodiments of the microfluidic device describedherein allow for a more reproducible and controllable interdigitation ofdroplets of specific liquids followed by pair-wise coalescence of thesedroplets, described in further detail herein. The droplet pairs cancontain liquids of different compositions and/or volumes, which wouldthen combine to allow for a specific reaction to be investigated. Thepair of droplets can come from any of the following: (i) two continuousaqueous streams and an oil stream; (ii) a continuous aqueous stream, anemulsion stream, and an oil stream, or (iii) two emulsion streams and anoil stream. The term “interdigitation” as used herein means pairing ofdroplets from separate aqueous streams, or from two separate inletnozzles, for eventual coalescence.

Various nozzle designs enhance the interdigitation of droplets andfurther improves coalescence of droplets due to the better control ofthe interdigitation and smaller distance between pairs of droplets. Thegreater control over interdigitation allows for a perfect control overthe frequency of either of the droplets. To obtain the optimumoperation, the spacing between droplets and coupling of the droplets canbe adjusted by adjusting flow of any of the streams, viscosity of thestreams, nozzle design (including orifice diameter, the channel angle,and post-orifice neck of the nozzle). Examples of preferred nozzledesigns are as described in WO 2007/081385 and WO 2008/063227.

Reservoir/Well

A device of the invention can include a sample solution reservoir orwell or other apparatus for introducing a sample to the device, at theinlet module, which is typically in fluid communication with an inletchannel. Reservoirs and wells used for loading one or more samples ontothe microfluidic device of the present invention, include but are notlimited to, syringes, cartridges, vials, eppendorf tubes and cellculture materials (e.g., 96 well plates). A reservoir may facilitateintroduction of molecules or cells into the device and into the sampleinlet channel of each analysis unit.

Coalescence Module

The microfluidic device of the present invention also includes one ormore coalescence modules. A “coalescence module” is within or coincidentwith at least a portion of the main channel at or downstream of theinlet module where molecules, cells, small molecules or particlescomprised within droplets are brought within proximity of other dropletscomprising molecules, cells, small molecules or particles and where thedroplets in proximity fuse, coalesce or combine their contents. Thecoalescence module can also include an apparatus, for generating anelectric force.

The electric force exerted on the fluidic droplet may be large enough tocause the droplet to move within the liquid. In some cases, the electricforce exerted on the fluidic droplet may be used to direct a desiredmotion of the droplet within the liquid, for example, to or within achannel or a microfluidic channel (e.g., as further described herein),etc.

The electric field can be generated from an electric field generator,i.e., a device or system able to create an electric field that can beapplied to the fluid. The electric field generator may produce an ACfield (i.e., one that varies periodically with respect to time, forexample, sinusoidally, sawtooth, square, etc.), a DC field (i.e., onethat is constant with respect to time), a pulsed field, etc. Theelectric field generator may be constructed and arranged to create anelectric field within a fluid contained within a channel or amicrofluidic channel. The electric field generator may be integral to orseparate from the fluidic system containing the channel or microfluidicchannel, according to some embodiments. As used herein, “integral” meansthat portions of the components integral to each other are joined insuch a way that the components cannot be in manually separated from eachother without cutting or breaking at least one of the components.

Techniques for producing a suitable electric field (which may be AC, DC,etc.) are known to those of ordinary skill in the art. For example, inone embodiment, an electric field is produced by applying voltage acrossa pair of electrodes, which may be positioned on or embedded within thefluidic system (for example, within a substrate defining the channel ormicrofluidic channel), and/or positioned proximate the fluid such thatat least a portion of the electric field interacts with the fluid. Theelectrodes can be fashioned from any suitable electrode material ormaterials known to those of ordinary skill in the art, including, butnot limited to, silver, gold, copper, carbon, platinum, copper,tungsten, tin, cadmium, nickel, indium tin oxide (“ITO”), etc., as wellas combinations thereof.

Preferred electrodes and patterned electrically conductive layers aredescribed in WO 2007/081385 and WO 2008/063227 and can be associatedwith any module of the device (inlet module, coalescence module, mixingmodule, delay module, detection module and sorting module) to generatedielectric or electric forces to manipulate and control the droplets andtheir contents.

Effective control of uncharged droplets within microfluidic devices canrequire the generation of extremely strong dielectric field gradients.The fringe fields from the edges of a parallel plate capacitor canprovide an excellent topology to form these gradients. The microfluidicdevice according to the present invention can include placing a fluidicchannel between two parallel electrodes, which can result in a steepelectric field gradient at the entrance to the electrodes due to edgeeffects at the ends of the electrode pair. Placing these pairs ofelectrodes at a symmetric channel split can allow precise bi-directionalcontrol of droplet within a device. Using the same principle, only withasymmetric splits, can allow single ended control of the dropletdirection in the same manner. Alternatively, a variation on thisgeometry will allow precise control of the droplet phase by shifting.

Dielectrophoresis is believed to produce movement of dielectric objects,which have no net charge, but have regions that are positively ornegatively charged in relation to each other. Alternating,non-homogeneous electric fields in the presence of droplets and/orparticles, such as cells or molecules, cause the droplets and/orparticles to become electrically polarized and thus to experiencedielectrophoretic forces. Depending on the dielectric polarizability ofthe particles and the suspending medium, dielectric particles will moveeither toward the regions of high field strength or low field strength.For example, the polarizability of living cells depends on theircomposition, morphology, and phenotype and is highly dependent on thefrequency of the applied electrical field. Thus, cells of differenttypes and in different physiological states generally possess distinctlydifferent dielectric properties, which may provide a basis for cellseparation, e.g., by differential dielectrophoretic forces. Likewise,the polarizability of droplets also depends upon their size, shape andcomposition. For example, droplets that contain salts can be polarized.According to formulas provided in Fiedler, et al. Analytical Chemistry70, 1909-1915 (1998), individual manipulation of single dropletsrequires field differences (inhomogeneities) with dimensions close tothe droplets.

The term “dielectrophoretic force gradient” means a dielectrophoreticforce is exerted on an object in an electric field provided that theobject has a different dielectric constant than the surrounding media.This force can either pull the object into the region of larger field orpush it out of the region of larger field. The force is attractive orrepulsive depending respectively on whether the object or thesurrounding media has the larger dielectric constant.

Manipulation is also dependent on permittivity (a dielectric property)of the droplets and/or particles with the suspending medium. Thus,polymer particles, living cells show negative dielectrophoresis athigh-field frequencies in water. For example, dielectrophoretic forcesexperienced by a latex sphere in a 0.5 MV/m field (10 V for a 20 micronelectrode gap) in water are predicted to be about 0.2 piconewtons (pN)for a 3.4 micron latex sphere to 15 pN for a 15 micron latex sphere(Fiedler, et al. Analytical Chemistry, 70, 1909-1915 (1998)). Thesevalues are mostly greater than the hydrodynamic forces experienced bythe sphere in a stream (about 0.3 pN for a 3.4 micron sphere and 1.5 pNfor a 15 micron sphere). Therefore, manipulation of individual cells orparticles can be accomplished in a streaming fluid, such as in a cellsorter device, using dielectrophoresis. Using conventional semiconductortechnologies, electrodes can be microfabricated onto a substrate tocontrol the force fields in a microfabricated sorting device of theinvention. Dielectrophoresis is particularly suitable for moving objectsthat are electrical conductors. The use of AC current is preferred, toprevent permanent alignment of ions. Megahertz frequencies are suitableto provide a net alignment, attractive force, and motion over relativelylong distances. See U.S. Pat. No. 5,454,472.

The electric field generator can be constructed and arranged (e.g.,positioned) to create an electric field applicable to the fluid of atleast about 0.01 V/micrometer, and, in some cases, at least about 0.03V/micrometer, at least about 0.05 V/micrometer, at least about 0.08V/micrometer, at least about 0.1 V/micrometer, at least about 0.3V/micrometer, at least about 0.5 V/micrometer, at least about 0.7V/micrometer, at least about 1 V/micrometer, at least about 1.2V/micrometer, at least about 1.4 V/micrometer, at least about 1.6V/micrometer, or at least about 2 V/micrometer. In some embodiments,even higher electric field intensities may be used, for example, atleast about 2 V/micrometer, at least about 3 V/micrometer, at leastabout 5 V/micrometer, at least about 7 V/micrometer, or at least about10 V/micrometer or more.

As described, an electric field may be applied to fluidic droplets tocause the droplets to experience an electric force. The electric forceexerted on the fluidic droplets may be, in some cases, at least about10⁻¹⁶ N/micrometer³. In certain cases, the electric force exerted on thefluidic droplets may be greater, e.g., at least about 10⁻¹⁵N/micrometer³, at least about 10⁻¹⁴ N/micrometer³, at least about 10⁻¹³N/micrometer³, at least about 10⁻¹² N/micrometer³, at least about 10⁻¹¹N/micrometer³, at least about 10⁻¹⁰ N/micrometer³, at least about 10⁻⁹N/micrometer³, at least about 10⁻⁸ N/micrometer³, or at least about 10⁻⁷N/micrometer or more. The electric force exerted on the fluidicdroplets, relative to the surface area of the fluid, may be at leastabout 10⁻¹⁵ N/micrometer², and in some cases, at least about 10⁻¹⁴N/micrometer², at least about 10⁻¹³ N/micrometer², at least about 10⁻¹²N/micrometer², at least about 10⁻¹¹ N/micrometer², at least about 10⁻¹⁰N/micrometer², at least about 10⁻⁹ N/micrometer, at least about 10⁻⁸N/micrometer², at least about 10⁻⁷ N/micrometer², or at least about 10⁻⁶N/micrometer² or more. In yet other embodiments, the electric forceexerted on the fluidic droplets may be at least about 10⁻⁹ N, at leastabout 10⁻⁸ N, at least about 10⁻⁷ N, at least about 10⁻⁶ N, at leastabout 10⁻⁵ N, or at least about 10⁻⁴ N or more in some cases.

Channel Expansion Geometries

In preferred embodiments described herein, droplet coalescence ispresently carried out by having two droplet forming nozzles emittingdroplets into the same main channel. The size of the nozzles allow forone nozzle to form a large drop that fills the exhaust line while theother nozzle forms a drop that is smaller than the first. The smallerdroplet is formed at a rate that is less than the larger droplet rate,which insures that at most one small droplet is between big droplets.Normally, the small droplet will catch up to the larger one over arelatively short distance, but sometimes the recirculation zone behindthe large drop causes the small drop to separate from the large dropcyclically. In addition, the small drop occasionally does not catch upwith the large one over the distance between the nozzles and thecoalescing electrodes. Thus, in some situations is a need for a morerobust coalescence scheme.

Geometric alterations in the coalescence module can create a morerobust, reliable coalescence or fusing of droplets over a wider range ofsizes and flows. The solution to improve the performance is to place anexpansion in the main channel between the electrodes. Optionally, asmall constriction (neckdown) just before this expansion can be used tobetter align the droplets on their way into the coalescence point. Thisoptional neckdown can help center the small droplet in the channelstream lines, reducing the chance that it will flow around the largerdroplet prior to coalescing in the expansion. The electrode pair may beplaced on either one side of the channel or on both sides.

The expansion in the coalescing region allows for a dramatic catching upof the small drop to the large drop, as shown through micrographs takenon an operating device. The volume of the expansion is big enough toslow the large droplet down so that the small drop always catches up tothe large drop, but doesn't allow the next large drop to catch up andmake contact with the pair to be coalesced. The electrodes allow forcoalescence to take place when the drops are in contact with each otherand passing through the field gradient.

Detection Module

The microfluidic device of the present invention can also include one ormore detection modules. A “detection module” is a location within thedevice, typically within the main channel where molecules, cells, smallmolecules or particles are to be detected, identified, measured orinterrogated on the basis of at least one predetermined characteristic.The molecules, cells, small molecules or particles can be examined oneat a time, and the characteristic is detected or measured optically, forexample, by testing for the presence or amount of a reporter. Forexample, the detection module is in communication with one or moredetection apparatuses. The detection apparatuses can be optical orelectrical detectors or combinations thereof. Examples of suitabledetection apparatuses include optical waveguides, microscopes, diodes,light stimulating devices, (e.g., lasers), photo multiplier tubes, andprocessors (e.g., computers and software), and combinations thereof,which cooperate to detect a signal representative of a characteristic,marker, or reporter, and to determine and direct the measurement or thesorting action at the sorting module. However, other detectiontechniques can also be employed

The terms “detecting” or “determining,” as used herein, generally refersto the analysis or measurement of a species, for example, quantitativelyor qualitatively, and/or the detection of the presence or absence of thespecies. “Detecting or “determining” may also refer to the analysis ormeasurement of an interaction between two or more species, for example,quantitatively or qualitatively, or by detecting the presence or absenceof the interaction. Examples of suitable techniques include, but are notlimited to, spectroscopy such as infrared, absorption, fluorescence,UV/visible, FTIR (“Fourier Transform Infrared Spectroscopy”), or Raman;gravimetric techniques; ellipsometry; piezoelectric measurements;immunoassays; electrochemical measurements; optical measurements such asoptical density measurements; circular dichromism; light scatteringmeasurements such as quasielectric light scattering; polarimetry;refractometry; or turbidity measurements as described further herein.

A detection module is within, communicating or coincident with a portionof the main channel at or downstream of the inlet module and, in sortingembodiments, at, proximate to, or upstream of, the sorting module orbranch point. The sorting module may be located immediately downstreamof the detection module or it may be separated by a suitable distanceconsistent with the size of the molecules, the channel dimensions andthe detection system. Precise boundaries for the detection module arenot required, but are preferred.

Sensors

One or more detections sensors and/or processors may be positioned to bein sensing communication with the fluidic droplet. “Sensingcommunication,” as used herein, means that the sensor may be positionedanywhere such that the fluidic droplet within the fluidic system (e.g.,within a channel), and/or a portion of the fluidic system containing thefluidic droplet may be sensed and/or determined in some fashion. Forexample, the sensor may be in sensing communication with the fluidicdroplet and/or the portion of the fluidic system containing the fluidicdroplet fluidly, optically or visually, thermally, pneumatically,electronically, or the like. The sensor can be positioned proximate thefluidic system, for example, embedded within or integrally connected toa wall of a channel, or positioned separately from the fluidic systembut with physical, electrical, and/or optical communication with thefluidic system so as to be able to sense and/or determine the fluidicdroplet and/or a portion of the fluidic system containing the fluidicdroplet (e.g., a channel or a microchannel, a liquid containing thefluidic droplet, etc.). For example, a sensor may be free of anyphysical connection with a channel containing a droplet, but may bepositioned so as to detect electromagnetic radiation arising from thedroplet or the fluidic system, such as infrared, ultraviolet, or visiblelight. The electromagnetic radiation may be produced by the droplet,and/or may arise from other portions of the fluidic system (orexternally of the fluidic system) and interact with the fluidic dropletand/or the portion of the fluidic system containing the fluidic dropletin such as a manner as to indicate one or more characteristics of thefluidic droplet, for example, through absorption, reflection,diffraction, refraction, fluorescence, phosphorescence, changes inpolarity, phase changes, changes with respect to time, etc. As anexample, a laser may be directed towards the fluidic droplet and/or theliquid surrounding the fluidic droplet, and the fluorescence of thefluidic droplet and/or the surrounding liquid may be determined.“Sensing communication,” as used herein may also be direct or indirect.As an example, light from the fluidic droplet may be directed to asensor, or directed first through a fiber optic system, a waveguide,etc., before being directed to a sensor.

Non-limiting examples of detection sensors useful in the inventioninclude optical or electromagnetically-based systems. For example, thesensor may be a fluorescence sensor (e.g., stimulated by a laser), amicroscopy system (which may include a camera or other recordingdevice), or the like. As another example, the sensor may be anelectronic sensor, e.g., a sensor able to determine an electric field orother electrical characteristic. For example, the sensor may detectcapacitance, inductance, etc., of a fluidic droplet and/or the portionof the fluidic system containing the fluidic droplet. In some cases, thesensor may be connected to a processor, which in turn, cause anoperation to be performed on the fluidic droplet, for example, bysorting the droplet.

Characteristics

Characteristics determinable with respect to the droplet and usable inthe invention can be identified by those of ordinary skill in the art.Non-limiting examples of such characteristics include fluorescence,spectroscopy (e.g., optical, infrared, ultraviolet, etc.),radioactivity, mass, volume, density, temperature, viscosity, pH,concentration of a substance, such as a biological substance (e.g., aprotein, a nucleic acid, etc.), or the like.

A corresponding signal is then produced, for example indicating that“yes” the characteristic is present, or “no” it is not. The signal maycorrespond to a characteristic qualitatively or quantitatively. That is,the amount of the signal can be measured and can correspond to thedegree to which a characteristic is present. For example, the strengthof the signal may indicate the size of a molecule, or the potency oramount of an enzyme expressed by a cell, or a positive or negativereaction such as binding or hybridization of one molecule to another, ora chemical reaction of a substrate catalyzed by an enzyme. In responseto the signal, data can be collected and/or a control system in thesorting module, if present, can be activated to divert a droplet intoone branch channel or another for delivery to the collection module orwaste module. Thus, in sorting embodiments, molecules or cells within adroplet at a sorting module can be sorted into an appropriate branchchannel according to a signal produced by the corresponding examinationat a detection module. The means of changing the flow path can beaccomplished through mechanical, electrical, optical, or some othertechnique as described herein.

A preferred detector is an optical detector, such as a microscope, whichmay be coupled with a computer and/or other image processing orenhancement devices to process images or information produced by themicroscope using known techniques. For example, molecules can beanalyzed and/or sorted by size or molecular weight. Enzymes can beanalyzed and/or sorted by the extent to which they catalyze chemicalreaction of a substrate (conversely, substrate can be analyzed and/orsorted by the level of chemical reactivity catalyzed by an enzyme).Cells can be sorted according to whether they contain or produce aparticular protein, by using an optical detector to examine each cellfor an optical indication of the presence or amount of that protein. Theprotein may itself be detectable, for example by a characteristicfluorescence, or it may be labeled or associated with a reporter thatproduces a detectable signal when the desired protein is present, or ispresent in at least a threshold amount. There is no limit to the kind ornumber of characteristics that can be identified or measured using thetechniques of the invention, which include without limitation surfacecharacteristics of the cell and intracellular characteristics, providedonly that the characteristic or characteristics of interest for sortingcan be sufficiently identified and detected or measured to distinguishcells having the desired characteristic(s) from those which do not. Forexample, any label or reporter as described herein can be used as thebasis for analyzing and/or sorting molecules or cells, i.e. detectingmolecules or cells to be collected.

Fluorescence Polarization/Fluorescence Lifetime

As described herein, the biological/chemical entity to be analyzed mayitself be detectable, for example by a characteristic fluorescence, orit may be labeled or associated with a reporter that produces adetectable signal when the desired protein is present, or is present inat least a threshold amount.

Luminescent colloidal semiconductor nanocrystals called quantum dots orq-dots (QD) are inorganic fluorophores that have the potential tocircumvent some of the functional limitations encountered by organicdyes. In particular, CdSe—ZnS core-shell QDs exhibit size-dependenttunable photoluminescence (PL) with narrow emission bandwidths (FWHM ˜30to 45 nm) that span the visible spectrum and broad absorption bands.These allow simultaneous excitation of several particle sizes (colors)at a common wavelength. This, in turn, allows simultaneous resolution ofseveral colors using standard instrumentation. CdSe—ZnS QDs also havehigh quantum yields, are resistant to photodegradation, and can bedetected optically at concentrations comparable to organic dyes.

Quantum dots are nano-scale semiconductors typically consisting ofmaterials such as crystalline cadmium selenide. The term ‘q-dot’emphasizes the quantum confinement effect of these materials, andtypically refers to fluorescent nanocrystals in the quantum confinedsize range. Quantum confinement refers to the light emission from bulk(macroscopic) semiconductors such as LEDs which results from excitingthe semiconductor either electrically or by shining light on it,creating electron-hole pairs which, when they recombine, emit light. Theenergy, and therefore the wavelength, of the emitted light is governedby the composition of the semiconductor material. If, however, thephysical size of the semiconductor is considerably reduced to be muchsmaller than the natural radius of the electron-hole pair (Bohr radius),additional energy is required to “confine” this excitation within thenanoscopic semiconductor structure leading to a shift in the emission toshorter wavelengths. Three different q-dots in several concentrationseach can be placed in a microdroplet, and can then be used with amicrofluidic device to decode what is in the drop. The Q-dot readoutextension to the fluorescence station can be incorporated into thedesign of the microfluidic device. A series of dichroic beamsplitters,emission filters, and detectors can be stacked onto the system, allowingmeasurement of the required five emission channels (two fluorescencepolarization signals and three q-dot bands).

Fluorescence Polarization (FP) detection technology enables homogeneousassays suitable for high throughput screening assays in the DrugDiscovery field. The most common label in the assays is fluorescein. InFP-assay the fluorophore is excited with polarized light. Onlyfluorophores parallel to the light absorb and are excited. The excitedstate has a lifetime before the light emission occurs. During this timethe labeled fluorophore molecule rotates and the polarization of thelight emitted differs from the excitation plane. To evaluate thepolarization two measurements are needed: the first using a polarizedemission filter parallel to the excitation filter (S-plane) and thesecond with a polarized emission filter perpendicular to the excitationfilter (P-plane). The Fluorescence Polarization response is given as mP(milli-Polarization level) and is obtained from the equation:Polarization (mP)=1000*(S−G*P)/(S+G*P)

Where S and P are background subtracted fluorescence count rates and G(grating) is an instrument and assay dependent factor.

The rotational speed of a molecule is dependent on the size of themolecule, temperature and viscosity of the solution. Fluorescein has afluorescence lifetime suitable for the rotation speeds of molecules inbio-affinity assays like receptor-ligand binding assays or immunoassaysof haptens. The basic principle is that the labeled compound is smalland rotates rapidly (low polarization). When the labeled compound bindsto the larger molecule, its rotation slows down considerably(polarization changes from low to high polarization). Thus, FP providesa direct readout of the extent of tracer binding to protein, nucleicacids, and other biopolymers.

Fluorescence polarization technology has been used in basic research andcommercial diagnostic assays for many decades, but has begun to bewidely used in drug discovery only in the past six years. Originally, FPassays for drug discovery were developed for single-tube analyticalinstruments, but the technology was rapidly converted to high-throughputscreening assays when commercial plate readers with equivalentsensitivity became available. These assays include such well-knownpharmaceutical targets such as kinases, phosphatases, proteases,G-protein coupled receptors, and nuclear receptors. Other homogeneoustechnologies based on fluorescence intensity have been developed. Theseinclude energy transfer, quenching, and enhancement assays. FP offersseveral advantages over these. The assays are usually easier toconstruct, since the tracers do not have to respond to binding byintensity changes. In addition, only one tracer is required and crudereceptor preparations may be utilized. Furthermore, since FP isindependent of intensity, it is relatively immune to colored solutionsand cloudy suspensions. FP offers several advantages in the area ofinstrumentation. Because FP is a fundamental property of the molecule,and the reagents are stable, little or no standardization is required.FP is relatively insensitive to drift in detector gain settings andlaser power.

The dyes chosen for FP are commonly used in most cell- and enzyme-basedassays and are designed not to overlap significantly with the q-dots.The dyes are evaluated both independently and together with the q-dots(at first off-instrument) to assess the cross-talk. Preferably, theliquid q-dot labels are read outside a spectral wavelength bandcurrently used in FACS analysis and sorting (i.e., the dyes flourescein,Cy3, Cy5, etc). This permits the use of currently-available assays(dependent on these dyes). Using specific q-dots, crosstalk isminimized.

Accordingly, the present invention provides methods to label dropletsand/or nanoreactors formed on a microfluidic device by using only asingle dye code to avoid cross-talk with other dyes during FP.Additionally, the present invention provides methods to create FP dyecodes to label compounds contained within liquids (including dropletsand/or nanoreactors) where the compound is designed to be differentiatedby FP on a microfluidic device. In this manner, dye codes having thesame color, absorption, and emission could be used to label compoundswithin liquids.

In one aspect, the present invention is directed to the use offluorescence polarization to label liquids. Droplets can be labeledusing several means. These labeling means include, but are not limitedto, the use of different dyes, quantum dots, capacitance, opacity, lightscattering, fluorescence intensity (FI), fluorescence lifetime (FL),fluorescence polarization (FP), circular dichroism (CD), fluorescencecorrelation and combinations of all of these previous labeling means.The following disclosure describes the use of FP and FI as a means tolabel droplets on a microfluidic device. In addition, the use of FL as ameans to adjust the overall FP of a solution, and by varying theconcentration of the total FI, to create a 2-dimensional encoding schemeis demonstrated.

In general, molecules that take up more volume will tumble slower than asmaller molecule coupled to the same fluorophore. FP is independent ofthe concentration of the dye; liquids can have vastly differentconcentrations of FITC in them yet still have identical FP measurements.

In a preferred embodiment, a FP dye is an organic dye that does notinterfere with the assay dye is used. Furthermore, since the totalintensity of the FP dye can be quantified, a second dimension in whichto label the droplet is provided. Thus, one can exploit the differencesin FP to create an encoding scheme of dye within a liquid solution,including droplets. Examples of ways to exploit the differences in FPare described in WO 2007/081385 and WO 2008/063227. In a singledimension, FP can be used to create an encoding scheme. However, thepresent invention can also use Fluorescence Intensity (FI) of theoverall solution to create even more labels in a second dimension.Interestingly, the differences of the fluorescence lifetime (FL) of twodyes with spectral overlap in the detected emission wavelength to changethe overall FP of the combined solution can also be exploited.

Although the use of multiple compounds to which a dye molecule isattached to span a range of FP can be utilized, it is also possible tospan the range using a high and low molecular weight compound set. Forexample, a dye can be attached to a large compound (for examplestreptavidin) and kept at a fixed concentration, to which a smallercompound (for example, a free dye molecule) would be titrated into thesame solution. The FP of the solution can be adjusted to be indiscernable increments from the value of the large molecule to somewhereslightly greater than the FP of the smaller molecule. The [total] dyeintensity can be varied by varying the concentration of the mixture ofthe two dye-attached compounds. By varying total dye concentration andthe FP, two dimensions can be used to generate the FP dye codes(FPcodes). Accordingly, many FPcodes can be generated using only twocompounds.

This could also include use of large fluorescent proteins such as GFPand the phycobiliproteins combined with a smaller molecule.

Examples of dyes commonly used in biological dyes are listed in Table 2below.

TABLE 2 Excitation Emission Examples of Wavelength Wavelength CompatibleDyes 450 500 Cyan 500 483 533 SYBR Green, FAM 523 568 HEX, VIC 558 610RED 610 615 640 RED 640 650 670 CY5

In another aspect, the present invention is directed labeling solidsusing properties other than dye emission and dye concentration. In oneembodiment the solid can include, for example, a bead or location on asolid support or chip. As demonstrated above for liquids, FI and FL canbe two of many dimensions of characteristics used as labels. By way ofnon-limiting example, it is possible to use two dyes with different FLto change the overall FP for a solid such as a bead or other mobilesolid support.

In another embodiment, a linker can be used to couple the dye to thebead. The linker can be varied so as to allow the dye to have differingdegrees of freedom in which to rotate (i.e., tumble). Varying the linkerin this manner can change the FP of the attached dye, which in uniquecombinations can be used as a label. In some embodiments, the beads canbe swollen in organic solvent and the dyes held in place by hydrophobicforces. In this case, the FP, FI, FL methods described above for liquidlabeling can also be used as a means for labeling the beads. A quenchingmolecule can also be used to change the characteristics of a dye. Suchquenching can be continuous or brought about through the interaction ofa molecule, such as a peptide or nucleic acid linker, with differingmeans of bringing molecules together depending on the strength oflinker-internal interaction (e.g., a nucleotide stem loop structure ofvarying lengths).

The reactions analyzed on the virtual, random and non-random arrays(discussed briefly below) can be also increased beyond the two (cy3 andcy5 intensities) commonly used for multiplexing. For example, differentFP, FI, etc can be used as a read-out.

Random array decoding: Beads of the prior art use one or morepre-attached oligonucleotide-coupled beads that are held in place in afiber-optic faceplate (for example, those used by Illumina). The oligoson the beads are decoded using sequential hybridization of a labeledcomplementary oligo. The assay of the prior art uses a separateoligonucleotide complementary zipcode (‘Illumacode’) attached to eachtype of bead.

The invention described herein is superior to the methods of the priorart in that the FP, FI, FL-labeled bead or mobile solid support can beplaced into a random array (e.g., a chip as manufactured by Illumina)and the FP, FI, FL used to decode the bead. The FP, FI, FL of the beadcan be decoded before using the chip and the different beads ‘mapped’ asto their specific locations. Alternatively, the bead can be decodedduring attachment of the assay read-out. Significantly, the methodsdescribed by the present invention can be used to pre-determine thelocation of each bead-type either before, or during analysis.

Virtual array decoding: Methods of the prior art use 2 lasers and 3detectors to differentiate a set of 100 bead-types. The beads-types aredifferentiated by the FI of two different dyes present in 1 of 10concentrations (per dye) contained within the bead, and the assaydetector is used to measure fluorescein concentration on the bead. Thedyes, which are added to organic-solvent swollen beads, are not directlyattached to the beads, but remain held within the bead by hydrophobicforces.

Using the methods of the present invention as described herein, a seconddetector to the machines of the prior art used to measure FP can beadded, thereby adding a third dimension and extending the encodingscheme beyond the 100 available in the prior art.

Non-random array decoding: In chips of the prior art (such as those usedby Affymetrix) oligonucleotides are synthesized directly on the chip.Decoding is simply a matter of knowing the location of the assay on thechip.

The methods as described herein can be advantageously used inconjunction with such chips to increase the number of things that can besimultaneously analyzed (i.e., multiplexed) on the chip. By way ofnon-limiting example, Cy3, Cy5, FL and FP can be used as analysismarkers for hybridization reactions.

The present invention also provides methods for labeling micro ornano-sized droplets using Radio Frequency Identification (RFID). RFIDtags can improve the identification of the contents within the droplets.Preferably, the droplets are utilized within a microfluidic device.

RFID is an automatic identification method, relying on storing andremotely retrieving data using devices called RFID tags or transponders.An RFID tag is an object that can be attached to or incorporated into aproduct, animal, or person for the purpose of identification using radiowaves. Chip-based RFID tags contain silicon chips and antennae. Passivetags require no internal power source, whereas active tags require apower source. Hitachi has “powder” 0.05 mm×0.05 mm RFID chips. The newchips are 64 times smaller than the previous record holder, the 0.4mm×0.4 mm mu-chips, and nine times smaller than Hitachi's last yearprototype, and have room for a 128-bit ROM that can store a unique38-digit ID number.

In one embodiment, a solution containing RFID tags are emulsified intodroplets and are used as a label for the identification of the materialwithin the droplet solution. Applications include, but are not limitedto; genetics, genomics, proteomics, chemical synthesis, biofuels, andothers.

In some embodiments, fluorescent polarization is used for digitalassays. In this method, positive (enzyme-containing) droplets areidentified and counted using changes in the fluorescence polarization offluorescent molecules in the droplets. Fluorescence polarization (FP)detection technology can use a label such as fluorescein. In an FP-assaythe fluorophore is excited with polarized light. Only fluorophoresparallel to the light absorb and are excited. The excited state has alifetime before the light emission occurs. During this time the labeledfluorophore molecule rotates and the polarization of the light emitteddiffers from the excitation plane. In some embodiments, to evaluate thepolarization two measurements are used: the first using a polarizedemission filter parallel to the excitation filter (S-plane) and thesecond with a polarized emission filter perpendicular to the excitationfilter (P-plane). Fluorescence Lifetime (FL) changes can be detectedbased on the chemical environment of the fluorophore such that bound andunbound antibodies can be distinguished by FL measurements well known toone skilled in the art.

The rotational speed of a molecule is dependent on the size of themolecule, temperature and viscosity of the solution. The principle hereis that the labeled compound is small and rotates rapidly (lowpolarization). When the labeled compound binds to the larger molecule,its rotation slows down considerably (polarization changes from low tohigh polarization). In general, molecules that take up more volume willtumble slower than a smaller molecule coupled to the same fluorophore.FP is independent of the concentration of the dye; liquids can havevastly different concentrations of FITC in them yet still have identicalFP measurements. Thus, FP provides a direct readout of the extent ofbinding to protein, nucleic acids, and other biopolymers or targets.

FP offers advantages in the context of multiplexing (discussed in moredetail elsewhere herein). Since FP is independent of intensity, it isrelatively immune to colored solutions and cloudy suspensions. FP offersseveral advantages in the area of instrumentation. Because FP is afundamental property of the molecule, and the reagents are stable,little or no standardization is required.

The dyes chosen for FP include any suitable dye such as, for example,fluorescein, Cy3, Cy5, etc. Suitable dyes include (name followed by[excitation wavelength, emission wavelength]): Cyan 500 [450, 500]; SYBRGreen, FAM [483, 533], HEX, VIC [523, 568]; RED 610 [558, 610]; RED 640[615, 640]; and CY5 [650, 670].

In some embodiments, an FP dye is an organic dye that does not interferewith other labels or dyes in an assay. Furthermore, since the totalintensity of the FP dye can be quantified, a second dimension in whichto label the partition is provided. Thus, one can exploit thedifferences in FP to create an encoding scheme of dye within a liquidsolution, including droplets. Examples of ways to exploit thedifferences in FP are described in WO 2007/081385 and WO 2008/063227.Fluorescence polarization is discussed in U.S. Pub. 2010/0022414, thecontents of which are hereby incorporated by reference in theirentirety.

In the example shown in FIG. 15A, the enzyme Src kinase (Src)phosphorylates a Src substrate peptide and creates a binding surface fora fluorescent reporter. A reporter construct containing the Src homology2 domain (SH2) and a fluorescein isothiocyanate (FITC) serves as afluorescent reporter (SH2-FITC). When SH2-FITC is added, it will bind tothe phosphorylated Src substrate peptide. FIG. 15B shows the samesequence of steps but in which Src substrate peptide is bound to a bead.

When the fluorescent reporter SH2-FITC is free in solution it has a lowfluorescence polarization, whereas when bound to a phosphorylatedpeptide (e.g., the last step shown in each of FIGS. 15A and 15B) it hasa measurably higher fluorescence polarization. Detection of fluorescentpolarization indicates a reaction-positive fluid partition. Many otherenzymes, binding motifs, and fluorescent reporters can be used.

Lasers

To detect a reporter or determine whether a molecule, cell or particlehas a desired characteristic, the detection module may include anapparatus for stimulating a reporter for that characteristic to emitmeasurable light energy, e.g., a light source such as a laser, laserdiode, light emitting diode (LED), high-intensity lamp, (e.g., mercurylamp), and the like. Where a lamp is used, the channels are preferablyshielded from light in all regions except the detection module. Where alaser is used, the laser can be set to scan across a set of detectionmodules from different analysis units. In addition, laser diodes orLED's may be microfabricated into the same chip that contains theanalysis units. Alternatively, laser diodes or LED's may be incorporatedinto a second chip (i.e., a laser diode chip) that is placed adjacent tothe analysis or microchip such that the laser light from the diodesshines on the detection module(s).

An integrated semiconductor laser and/or an integrated photodiodedetector can be included on the substrate in the vicinity of thedetection module. This design provides the advantages of compactness anda shorter optical path for exciting and/or emitted radiation, thusminimizing distortion and losses.

Fluorescence produced by a reporter is excited using a laser beamfocused on molecules (e.g., DNA, protein, enzyme or substrate) or cellspassing through a detection region. Fluorescent reporters can include,but are not limited to, rhodamine, fluorescein, Texas red, Cy 3, Cy 5,phycobiliprotein (e.g., phycoerythrin), green fluorescent protein (GFP),YOYO-1 and PicoGreen. In molecular fingerprinting applications, thereporter labels can be fluorescently labeled single nucleotides, such asfluorescein-dNTP, rhodamine-dNTP, Cy3-dNTP, etc.; where dNTP representsdATP, dTTP, dUTP or dCTP. The reporter can also be chemically-modifiedsingle nucleotides, such as biotin-dNTP. The reporter can befluorescently or chemically labeled amino acids or antibodies (whichbind to a particular antigen, or fragment thereof, when expressed ordisplayed by a cell or virus).

The device can analyze and/or sort cells based on the level ofexpression of selected cell markers, such as cell surface markers, whichhave a detectable reporter bound thereto, in a manner similar to thatcurrently employed using fluorescence-activated cell sorting (FACS)machines. Proteins or other characteristics within a cell, and which donot necessarily appear on the cell surface, can also be identified andused as a basis for sorting. The device can also determine the size ormolecular weight of molecules such as polynucleotides or polypeptides(including enzymes and other proteins) or fragments thereof passingthrough the detection module. Alternatively, the device can determinethe presence or degree of some other characteristic indicated by areporter. If desired, the cells, particles or molecules can be sortedbased on this analysis. The sorted cells, particles or molecules can becollected from the outlet channels in collection modules (or discardedin wasted modules) and used as needed. The collected cells, particles ormolecules can be removed from the device or reintroduced to the devicefor additional coalescence, analysis and sorting.

Processors

As used herein, a “processor” or a “microprocessor” is any component ordevice able to receive a signal from one or more sensors, store thesignal, and/or direct one or more responses (e.g., as described above),for example, by using a mathematical formula or an electronic orcomputational circuit. The signal may be any suitable signal indicativeof the environmental factor determined by the sensor, for example apneumatic signal, an electronic signal, an optical signal, a mechanicalsignal, etc.

The device of the present invention can comprise features, such asintegrated metal alloy components and/or features patterned in anelectrically conductive layer, for detecting droplets by broadcasting asignal around a droplet and picking up an electrical signal in proximityto the droplet.

Beads

The device of the present invention also comprises the use of beads andmethods for analyzing and sorting beads (i.e., bead reader device). Thedevice can read and either sort or not sort droplets containing one ormore of a set of two or more beads. Each bead can be differentiated fromeach other bead within a set. Beads can be separated by several tagsincluding, but not limited to, quantum dyes, fluorescent dyes, ratios offluorescent dyes, radioactivity, radio-tags, etc. For example, a set ofbeads containing a ratio of two dyes in discrete amounts with anapparatus for detecting and differentiating beads containing onediscrete ratio from the other beads in this set having a different ratioof the two dyes. The microfluidic device can include paramagnetic beads.The paramagnetic beads can introduce and remove chemical components fromdroplets using droplet coalescence and breakup events. The paramagneticbeads can also be used for sorting droplets.

The present invention provides methods of screening molecular librarieson beads through limited-dilution-loading and then chemical or opticalrelease inside of droplets. Provided are methods for chemical synthesison a bead and releasing said chemical attached to the bead using areleasing means (chemical, UV light, heat, etc) within a droplet, andthen combining a second droplet to the first droplet for furthermanipulation. For example, tea-bag synthesis of chemicals on a beadsimultaneously with a means for identifying said bead (using, forexample, a mass spec tag). Using the resulting mixed-chemistry beads ina droplet within a fluid flow, and exposing the beads to UV light torelease the chemical synthesized from the bead into the dropletenvironment. Combining the droplet containing the released chemical witha droplet containing a cell, and performing a cell-based assay. Sortingdroplets having the desired characteristics (for example, turn on of areporter gene), and then analyzing the sorted beads using massspectroscopy.

The device of the present invention can comprise column separation priorto bead sorting. A device containing a channel loaded with a separatingmeans for chromatographically sorting the sample prior to dropletformation. Such separating means could include size, charge,hydrophobicity, atomic mass, etc. The separating can be done isocraticor by use of a means for generating a gradient chemically, (for exampleusing salt or hydrophobicity), electrically, by pressure, or etc. Forexample, a channel is preloaded with Sepharose size exclusion media. Asample is loaded at one end, and the droplets are formed at an opposingend. The sample separates by size prior to becoming incorporated withina droplet.

Sorting Module

The microfluidic device of the present invention can further include oneor more sorting modules. A “sorting module” is a junction of a channelwhere the flow of molecules, cells, small molecules or particles canchange direction to enter one or more other channels, e.g., a branchchannel for delivery to an outlet module (i.e., collection or wastemodule), depending on a signal received in connection with anexamination in the detection module. Typically, a sorting module ismonitored and/or under the control of a detection module, and thereforea sorting module may “correspond” to such detection module. The sortingregion is in communication with and is influenced by one or more sortingapparatuses. A sorting apparatus comprises techniques or controlsystems, e.g., dielectric, electric, electro-osmotic, (micro-) valve,etc. A control system can employ a variety of sorting techniques tochange or direct the flow of molecules, cells, small molecules orparticles into a predetermined branch channel. A “branch channel” is achannel which is in communication with a sorting region and a mainchannel. The main channel can communicate with two or more branchchannels at the sorting module or “branch point”, forming, for example,a T-shape or a Y-shape. Other shapes and channel geometries may be usedas desired. Typically, a branch channel receives molecules, cells, smallmolecules or particles depending on the molecule, cells, small moleculesor particles characteristic of interest as detected by the detectionmodule and sorted at the sorting module. A branch channel can have anoutlet module and/or terminate with a well or reservoir to allowcollection or disposal (collection module or waste module, respectively)of the molecules, cells, small molecules or particles. Alternatively, abranch channel may be in communication with other channels to permitadditional sorting.

The device of the present invention can further include one or moreoutlet modules. An “outlet module” is an area of the device thatcollects or dispenses molecules, cells, small molecules or particlesafter coalescence, detection and/or sorting. The outlet module caninclude a collection module and/or a waste module. The collection modulecan be connected to a means for storing a sample. The collection modulecan be a well or reservoir for collecting and containing dropletsdetected to have a specific predetermined characteristic in thedetection module. The collection module can be temperature controlled.The waste module can be connected to a means for discarding a sample.The waste module can be a well or reservoir for collecting andcontaining droplets detected to not have a specific predeterminedcharacteristic in the detection module. The outlet module is downstreamfrom a sorting module, if present, or downstream from the detectionmodule if a sorting module is not present. The outlet module may containbranch channels or outlet channels for connection to a collection moduleor waste module. A device can contain more than one outlet module.

A characteristic of a fluidic droplet may be sensed and/or determined insome fashion, for example, as described herein (e.g., fluorescence ofthe fluidic droplet may be determined), and, in response, an electricfield may be applied or removed from the fluidic droplet to direct thefluidic droplet to a particular region (e.g. a channel). A fluidicdroplet is preferably sorted or steered by inducing a dipole in theuncharged fluidic droplet (which may be initially charged or uncharged),and sorting or steering the droplet using an applied electric field. Theelectric field may be an AC field, a DC field, etc. Methods of sortingor steering droplets in an electric field are as described in WO2006/040551; WO 2006/040554; WO 2004/002627; WO 2004/091763; WO2005/021151; WO 2006/096571; WO 2007/089541; WO 2007/081385 and WO2008/063227. Improvements in the efficiency, accuracy, and reliabilityof the preferred dielectric droplet sorting technique described aboveare possibly by utilizing additional channel and electrode geometries,as described in WO 2007/081385 and WO 2008/063227.

Alternately, a fluidic droplet may be directed by creating an electriccharge (e.g., as previously described) on the droplet, and steering thedroplet using an applied electric field, which may be an AC field, a DCfield, etc. As an example, an electric field maybe selectively appliedand removed (or a different electric field may be applied) as needed todirect the fluidic droplet to a particular region. The electric fieldmay be selectively applied and removed as needed, in some embodiments,without substantially altering the flow of the liquid containing thefluidic droplet. For example, a liquid may flow on a substantiallysteady-state basis (i.e., the average flowrate of the liquid containingthe fluidic droplet deviates by less than 20% or less than 15% of thesteady-state flow or the expected value of the flow of liquid withrespect to time, and in some cases, the average flowrate may deviateless than 10% or less than 5%) or other predetermined basis through afluidic system of the invention (e.g., through a channel or amicrochannel), and fluidic droplets contained within the liquid may bedirected to various regions, e.g., using an electric field, withoutsubstantially altering the flow of the liquid through the fluidicsystem.

In some embodiments, the fluidic droplets may be sorted into more thantwo channels. Alternately, a fluidic droplet may be sorted and/or splitinto two or more separate droplets, for example, depending on theparticular application. Any of the above-described techniques may beused to spilt and/or sort droplets. As a non-limiting example, byapplying (or removing) a first electric field to a device (or a portionthereof), a fluidic droplet may be directed to a first region orchannel; by applying (or removing) a second electric field to the device(or a portion thereof), the droplet may be directed to a second regionor channel; by applying a third electric field to the device (or aportion thereof), the droplet may be directed to a third region orchannel; etc., where the electric fields may differ in some way, forexample, in intensity, direction, frequency, duration, etc. In a seriesof droplets, each droplet may be independently sorted and/or split; forexample, some droplets may be directed to one location or another, whileother droplets may be split into multiple droplets directed to two ormore locations.

In some cases, high sorting speeds may be achievable using certainsystems and methods of the invention. For instance, at least about 1droplet per second may be determined and/or sorted in some cases, and inother cases, at least about 10 droplets per second, at least about 20droplets per second, at least about 30 droplets per second, at leastabout 100 droplets per second, at least about 200 droplets per second,at least about 300 droplets per second, at least about 500 droplets persecond, at least about 750 droplets per second, at least about 1000droplets per second, at least about 1500 droplets per second, at leastabout 2000 droplets per second, at least about 3000 droplets per second,at least about 5000 droplets per second, at least about 7500 dropletsper second, at least about 10,000 droplets per second, at least about15,000 droplets per second, at least about 20,000 droplets per second,at least about 30,000 droplets per second, at least about 50,000droplets per second, at least about 75,000 droplets per second, at leastabout 100,000 droplets per second, at least about 150,000 droplets persecond, at least about 200,000 droplets per second, at least about300,000 droplets per second, at least about 500,000 droplets per second,at least about 750,000 droplets per second, at least about 1,000,000droplets per second may be determined and/or sorted in such a fashion.

Sample Recovery

The present invention proposes methods for recovering aqueous phasecomponents from aqueous emulsions that have been collected on amicrofluidic device in a minimum number of steps and in a gentle mannerso as to minimize potential damage to cell viability.

In one aspect, a stable aqueous sample droplet emulsion containingaqueous phase components in a continuous phase carrier fluid is allowedto cream to the top of the continuous phase carrier oil. By way ofnonlimiting example, the continuous phase carrier fluid can include aperfluorocarbon oil that can have one or more stabilizing surfactants.The aqueous emulsion rises to the top or separates from the continuousphase carrier fluid by virtue of the density of the continuous phasefluid being greater than that of the aqueous phase emulsion. Forexample, the perfluorocarbon oil used in one embodiment of the device is1.8, compared to the density of the aqueous emulsion, which is 1.0.

The creamed emulsion is then placed onto a second continuous phasecarrier fluid which contains a de-stabilizing surfactant, such as aperfluorinated alcohol (e.g., 1H,1H,2H,2H-Perfluoro-1-octanol). Thesecond continuous phase carrier fluid can also be a perfluorocarbon oil.Upon mixing, the aqueous emulsion begins to coalesce, and coalescence iscompleted by brief centrifugation at low speed (e.g., 1 minute at 2000rpm in a microcentrifuge). The coalesced aqueous phase can now beremoved (cells can be placed in an appropriate environment for furtheranalysis).

Additional destabilizing surfactants and/or oil combinations can beidentified or synthesized to be useful with this invention.

Additional Modules

The microfluidic devices of the present invention can further includeone or more mixing modules, one or more delay modules, one or moreacoustic actuators and/or UV-release modules, as described in WO2007/081385 and WO 2008/063227.

Assays

The droplet generation rate, spacing and size of the water droplets madeon a microfluidic device are tuned to the desired size, such aspicoliter to nanoliter volumes. Additionally, droplet libraries of thepresent invention can be introduced back onto a medium for additionalprocessing. Multicomponent droplets can easily be generated by bringingtogether streams of materials at the point where droplets are made(co-flow). Alternatively, one can combine different droplets, eachcontaining individual reactants. This is achieved by selecting dropletsizes such that one droplet is roughly wider than the channel width andthe other droplet is smaller so that the small droplets rapidly catch upto the larger droplets. An electric field is then used to induce dipolesin the droplet pairs, forcing them to combine into a single droplet andpermitting them to intermix the contents.

Optics for fluorescence detection capable of measuring fluorophoreswithin the aqueous droplets, while simultaneously permitting visualmonitoring via a high speed video microscope. Specifically, threeseparate lasers provide excitation at 405 nm, 488 nm, and 561 nmwavelengths focused to a spot approximately 17 microns in diameter,illuminating each droplet as it enters the detection zone. The system isconfigured to detect emitted light using a series of photomultipliertubes, and is able to detect less than 10,000 FITC molecule equivalentsat a 5 kHz droplet rate.

A critical component for isolating sub-populations or rare cells from aheterogeneous cell mixture is a fluorescence-activated microfluidicdroplet sorter as described in greater detail herein. Sorting inmicrofluidic devices can be done using a dielectrophoretic force onneutral droplets. Providing an alternate means that can be preciselycontrolled, can be switched at high frequencies, and requires no movingparts. After the contents of individual droplets are probed in thefluorescence detection zone, selected droplets can be sorted intodiscreet streams for recovery and further processing.

A key feature for improving genomic characterization of theheterogeneous mixture of cell types present in a typical tissue orbiopsy would be the ability to fractionate the initial cell populationinto sub-populations, permitting analysis of rare cells and enablingmolecular correlation studies. The microfluidic device provides theability to sort cell-containing droplets based on fluorescent signals. Anumber of immediate uses for this capability include: 1) sortingcell-containing droplets away from empty droplets; 2) sortingsub-populations based on specific nucleic acid hybridization; 3) sortingsub-populations based on cell surface binding properties; 4) sortingsub-populations based on secreted activities or reporter enzymeproducts. A number of these approaches have already been tested inpreliminary experiments, using either bacterial or mammalian cells.

For example, Sort-on-Generation is a combination of modules thatgenerates single cell containing-droplets (along with approximately 10times more empty droplets, from Poisson distribution as described hereinand subsequently sorts the cell-containing droplets away from the emptydroplets, based on fluorescent signals.

Also, it has been demonstrated the ability to sort-on-generation usingDNA-intercalating dyes. This approach is enabled for any stained cell.

Determining the volume of an individual drop from a 2-D image in amicrofluidic channel can be accomplished relatively easily with toolstypically associated with microfluidics. The basic equipment needed are;simple optics with a camera, a fluorescent laser detector, amicrofluidic device, and pumps.

A 10 pt calibration is done by plotting the average projected area vs.the average volume of a drop. The average projected area is determinedby real-time image analysis of droplets during emulsion generation in aspecific region of the chip. This region is clearly marked and calledthe calibration region. Calibration is accomplished by simultaneouslylogging the projected area of individual droplets for 60 s andcalculating the average, and using a laser is to count the total numberof droplets that pass through the channel at the calibration region.From this count, one can determine the average frequency and the averagevolume of a droplet.

Where,

$\begin{matrix}{f = \frac{Drops}{t}} \\{\overset{\_}{V} = \frac{{F_{Buffer}\left\lbrack \frac{uL}{hr} \right\rbrack}*{10^{6}\left\lbrack \frac{pL}{uL} \right\rbrack}}{{f\left\lbrack \frac{Drops}{s} \right\rbrack}*{3600\left\lbrack \frac{s}{hr} \right\rbrack}}}\end{matrix}$

Plotting this data for all points yields a calibration curve.

During reinjection of an emulsion, using image analysis, one can log theprojected area of each individual droplet and estimate the volume ofeach droplet by using the calibration curve. From this data, one cancalculate the average volume and size distribution for a givenpopulation of droplets.

The microfluidic device of the present invention can be utilized toconduct numerous chemical and biological assays, including but notlimited to, creating emulsion libraries, flow cytometry, geneamplification, isothermal gene amplification, DNA sequencing, SNPanalysis, drug screening, RNAi analysis, karyotyping, creating microbialstrains with improved biomass conversion, moving cells using opticaltweezer/cell trapping, transformation of cells by electroporation, μTAS,and DNA hybridization.

PCR in Droplets

An emulsion library comprising at least a first aqueous droplet and atleast a second aqueous droplet within a fluorocarbon oil comprising atleast one fluorosurfactant, wherein the at least first and the at leastsecond droplets are uniform in size and wherein at least first dropletcomprises at least a first pair or oligonucleotides and the at leastsecond droplet comprises at least a second pair or oligonucleotides,wherein the first and second pair of oligonucleotides is different.

In an embodiment, the oligonucleotide is DNA; in another embodiment, theoligonucleotide is RNA. In a further embodiment, the oligonucleotide hasat least 5 nucleotides, e.g., 5 to 100, 10 to 90, 12 to 80, 14 to 70, 15to 60, 15 to 50, 15 to 40, 15 to 35, 15 to 30, 15 to 28, 15 to 25, 15 to23, and 15 to 20 nucleotides. In one embodiment, the twooligonucleotides in the pair of oligonucleotides have the same number ofnucleotides; in another embodiment, the two oligonucleotides in the pairof oligonucleotides have different number of nucleotides.

The present invention provides a method for amplifying a genomic DNA,comprising (a) providing a first sample fluid wherein said first samplefluid comprises an emulsion library comprising at least a first aqueousdroplet and at least a second aqueous droplet within a fluorocarbon oilcomprising at least one fluorosurfactant, wherein the at least first andthe at least second droplets are uniform in size and wherein at leastfirst droplet comprises at least a first pair or oligonucleotides andthe at least second droplet comprises at least a second pair oroligonucleotides, wherein the first and second pair of oligonucleotidesis different; (b) providing a second sample fluid wherein said secondsample fluid comprises a plurality of aqueous droplets comprising saidgenomic DNA within an immiscible fluorocarbon oil comprising at leastone fluorosurfactant; (c) providing a microfluidic substrate comprisingat least two inlet channels adapted to carry at least two dispersedphase sample fluids and at least one main channel adapted to carry atleast one continuous phase fluid; (d) flowing the first sample fluidthrough a first inlet channel which is in fluid communication with saidmain channel at a junction, wherein said junction comprises a firstfluidic nozzle designed for flow focusing such that said first samplefluid forms a plurality of droplets of a first uniform size in saidcontinuous phase; (e) flowing the second sample fluid through a secondinlet channel which is in fluid communication with said main channel ata junction, wherein said junction comprises a second fluidic nozzledesigned for flow focusing such that said second sample fluid forms aplurality of droplets of a second uniform size in said continuous phase,wherein the size of the droplets of the second sample fluid are smallerthan the size of the droplets of the first sample fluid; (f) providing aflow and droplet formation rate of the first and second sample fluidswherein the droplets are interdigitized such that a first sample fluiddroplet is followed by and paired with a second sample fluid droplet;(g) providing channel dimensions such that the paired first sample fluidand the second sample fluid droplet are brought into proximity; (h)coalescing the paired first and second sample droplets as the paireddroplets pass through an electric field, and (i) amplifying said genomicDNA comprised within the coalesced droplets.

A unique feature of the described droplet-based microfluidic approachfor working with nucleic acids is that it uses immiscibleoil-encapsulated aqueous droplets to shield the DNA from the innersurfaces of the microfluidic chip, with a surfactant interfaceseparating the aqueous droplet and its contents from the surroundingimmiscible fluorocarbon oil. Therefore, DNA amplification reactionsoccurring inside these droplets generate material that does not interactwith the channel walls, and collection of the DNA-containing dropletsfor subsequent manipulation and sequencing is straightforward. Thistechnology provides a solution for amplification of DNA from singlecells, allowing for both genotyping and whole genome amplification.

Evidence shows that specific loci can be amplified by PCR in dropletsgenerated on the microfluidic device, either by performing PCR on-chip(with droplets moving through a serpentine channel across severaldifferent temperatures under microfluidic control), or by placing thecollected droplets into a standard thermocycler. Droplets generatedcontaining DNA and reagents required for PCR-based amplification(thermostable polymerase, dNTPs, Mg, appropriate buffer) have beendemonstrated to be extremely robust, showing high stability for bothon-chip and off-chip (standard thermocycler) amplification. Each dropletremains intact and separate during cycling, including during thedenaturation steps at 98° C. In one embodiment, a microfluidic device asdescribed herein, fuses droplets with individual primer pairs for PCRamplification and preparation of many exons in parallel for highthroughput re-sequencing.

Antibodies and ELISA

The present invention provides a method for performing an ELISA assay,comprising (a) providing a first sample fluid wherein said first samplefluid comprises an emulsion library comprising a plurality of aqueousdroplets within an immiscible fluorocarbon oil comprising at least onefluorosurfactant, wherein each droplet is uniform in size and comprisesat least a first antibody, and a single element linked to at least asecond antibody, wherein said first and second antibodies are different;(b) providing a second sample fluid wherein said second sample fluidcomprises a plurality of aqueous droplets within an immisciblefluorocarbon oil comprising at least one fluorosurfactant, said dropletscomprising a test fluid; (c) providing a third sample fluid wherein saidthird sample fluid comprises a plurality of aqueous droplets within animmiscible fluorocarbon oil comprising at least one fluorosurfactant,said droplets comprising at least one enzyme; (d) providing a fourthsample fluid wherein said fourth sample fluid comprises a plurality ofaqueous droplets within an immiscible fluorocarbon oil comprising atleast one fluorosurfactant, said droplets comprising at least onesubstrate; (e) providing a microfluidic substrate comprising at leasttwo inlet channels adapted to carry at least two dispersed phase samplefluids and at least one main channel adapted to carry at least onecontinuous phase fluid; (f) flowing the first sample fluid through afirst inlet channel which is in fluid communication with said mainchannel at a junction, wherein said junction comprises a first fluidicnozzle designed for flow focusing such that said first sample fluidforms a plurality of droplets of a first uniform size in said continuousphase; (g) flowing the second sample fluid through a second inletchannel which is in fluid communication with said main channel at ajunction, wherein said junction comprises a second fluidic nozzledesigned for flow focusing such that said second sample fluid forms aplurality of droplets of a second uniform size in said continuous phase,wherein the size of the droplets of the second sample fluid are smallerthan the size of the droplets of the first sample fluid; (h) providing aflow and droplet formation rate of the first and second sample fluidswherein the droplets are interdigitized such that a first sample fluiddroplet is followed by and paired with a second sample fluid droplet;(i) providing channel dimensions such that the paired first sample fluidand the second sample fluid droplet are brought into proximity; (j)coalescing the paired first and second sample droplets as the paireddroplets pass through an electric field, forming at least a firstcoalesced droplet; (k) flowing the third sample fluid through a thirdinlet channel which is in fluid communication with said main channel ata junction, wherein said junction comprises a third fluidic nozzledesigned for flow focusing such that said third sample fluid forms aplurality of droplets of a third uniform size in said continuous phase,wherein the size of the droplets of the third sample fluid are smallerthan the size of the droplets of at least first coalesced droplet; (l)providing a flow and droplet formation rate of the third sample fluidwherein the third sample fluid droplet and at least first coalesceddroplet are interdigitized such that the at least first coalesceddroplet is followed by and paired with the third sample fluid droplet;(m) providing channel dimensions such that the paired at least firstcoalesced droplet and the third sample fluid droplet are brought intoproximity; (n) coalescing the paired at least first coalesced dropletand third sample droplets as the paired droplets pass through anelectric field, forming at least a second coalesced droplet; (o) flowingthe fourth sample fluid through a fourth inlet channel which is in fluidcommunication with said main channel at a junction, wherein saidjunction comprises a fourth fluidic nozzle designed for flow focusingsuch that said fourth sample fluid forms a plurality of droplets of afourth uniform size in said continuous phase, wherein the size of thedroplets of the fourth sample fluid are smaller than the size of thedroplets of at least second coalesced droplet; (p) providing a flow anddroplet formation rate of the fourth sample fluid wherein the fourthsample fluid droplet and at least second coalesced droplet areinterdigitized such that the at least second coalesced droplet isfollowed by and paired with the fourth sample fluid droplet; (q)providing channel dimensions such that the paired at least secondcoalesced droplet and the fourth sample fluid droplet are brought intoproximity; (r) coalescing the paired at least second coalesced dropletand fourth sample droplets as the paired droplets pass through anelectric field, forming at least a third coalesced droplet, and (s)detecting the conversion of said substrate to a product by said enzymewithin the at least a third coalesced droplet.

The present invention also provides a method for performing an ELISAassay, comprising (a) providing a first sample fluid wherein said firstsample fluid comprises an emulsion library comprising a plurality ofaqueous droplets within an immiscible fluorocarbon oil comprising atleast one fluorosurfactant, wherein each droplet is uniform in size andcomprises at least a first element linked to at least a first antibody,and at least a second element linked to at least a second antibody,wherein said first and second antibodies are different; (b) providing asecond sample fluid wherein said second sample fluid comprises aplurality of aqueous droplets within an immiscible fluorocarbon oilcomprising at least one fluorosurfactant, said droplets comprising atest fluid (c) providing a third sample fluid wherein said third samplefluid comprises a plurality of aqueous droplets within an immisciblefluorocarbon oil comprising at least one fluorosurfactant, said dropletscomprising at least one substrate; (d) providing a microfluidicsubstrate comprising at least two inlet channels adapted to carry atleast two dispersed phase sample fluids and at least one main channeladapted to carry at least one continuous phase fluid; (e) flowing thefirst sample fluid through a first inlet channel which is in fluidcommunication with said main channel at a junction, wherein saidjunction comprises a first fluidic nozzle designed for flow focusingsuch that said first sample fluid forms a plurality of droplets of afirst uniform size in said continuous phase; (f) flowing the secondsample fluid through a second inlet channel which is in fluidcommunication with said main channel at a junction, wherein saidjunction comprises a second fluidic nozzle designed for flow focusingsuch that said second sample fluid forms a plurality of droplets of asecond uniform size in said continuous phase, wherein the size of thedroplets of the second sample fluid are smaller than the size of thedroplets of the first sample fluid; (g) providing a flow and dropletformation rate of the first and second sample fluids wherein thedroplets are interdigitized such that a first sample fluid droplet isfollowed by and paired with a second sample fluid droplet; (h) providingchannel dimensions such that the paired first sample fluid and thesecond sample fluid droplet are brought into proximity; (i) coalescingthe paired first and second sample droplets as the paired droplets passthrough an electric field, forming at least a first coalesced droplet,wherein if the two antibodies bind an antigen in the test sample the atleast first and at least second elements interact to form a functionalenzyme; (j) flowing the third sample fluid through a third inlet channelwhich is in fluid communication with said main channel at a junction,wherein said junction comprises a third fluidic nozzle designed for flowfocusing such that said third sample fluid forms a plurality of dropletsof a third uniform size in said continuous phase, wherein the size ofthe droplets of the third sample fluid are smaller than the size of thedroplets of at least first coalesced droplet; (k) providing a flow anddroplet formation rate of the third sample fluid wherein the thirdsample fluid droplet and at least first coalesced droplet areinterdigitized such that the at least first coalesced droplet isfollowed by and paired with the third sample fluid droplet; (l)providing channel dimensions such that the paired at least firstcoalesced droplet and the third sample fluid droplet are brought intoproximity; (m) coalescing the paired at least first coalesced dropletand third sample droplets as the paired droplets pass through anelectric field, forming at least a second coalesced droplet, and (n)detecting the conversion of said substrate to a product by said enzymewithin the at least a second coalesced droplet.

Small sample volumes are needed in performing immunoassays. Non-limitingexamples include cases where the sample is precious or limited, i.e.,serum archives, tissue banks, and tumor biopsies. Immunoassays wouldideally be run in droplets where only 10 to 100 pL of sample wereconsumed for each assay. Specifically, the lack of a robust convenientwash step has prevented the development of ELISA assays in droplets. Thepresent invention provides for methods in which beads can be used toperform ELISA assays in aqueous droplets within channels on amicrofluidic device. The advantage of utilizing microfluidic devices isit greatly reduces the size of the sample volume needed. Moreover, abenefit of droplet based microfluidic methods is the ability to runnumerous assays in parallel and in separate micro-compartments.

In the examples shown herein, there are several non-limiting read-outsthat can be applied to signal amplification in a microfluidic device.The amplification methods include enzyme amplification and rollingcircle amplification of signal that uses a nucleic-acid intermediate. Inaddition, a non-enzymatic means for signal amplification can also beused.

Cell Libraries

The present invention provides a method for generating an enzymelibrary, comprising (a) providing a first sample fluid wherein saidfirst sample fluid comprises an emulsion library comprising a pluralityof aqueous droplets within an immiscible fluorocarbon oil comprising atleast one fluorosurfactant, said droplets comprising at least one celltransformed with at least one nucleic acid molecule encoding for anenzyme, wherein said cells replicate within said droplets therebysecreting produced enzymes within the droplets; (b) providing a secondsample fluid wherein said second sample fluid comprises a plurality ofaqueous droplets within an immiscible fluorocarbon oil comprising atleast one fluorosurfactant, said droplets comprising at least onesubstrate; (c) providing a microfluidic substrate comprising at leasttwo inlet channels adapted to carry at least two dispersed phase samplefluids and at least one main channel adapted to carry at least onecontinuous phase fluid; (d) flowing the first sample fluid through afirst inlet channel which is in fluid communication with said mainchannel at a junction, wherein said junction comprises a first fluidicnozzle designed for flow focusing such that said first sample fluidforms a plurality of droplets of a first uniform size in said continuousphase; (e) flowing the second sample fluid through a second inletchannel which is in fluid communication with said main channel at ajunction, wherein said junction comprises a second fluidic nozzledesigned for flow focusing such that said second sample fluid forms aplurality of droplets of a second uniform size in said continuous phase,wherein the size of the droplets of the second sample fluid are smallerthan the size of the droplets of the first sample fluid; (f) providing aflow and droplet formation rate of the first and second sample fluidswherein the droplets are interdigitized such that a first sample fluiddroplet is followed by and paired with a second sample fluid droplet;(g) providing channel dimensions such that the paired first sample fluidand the second sample fluid droplet are brought into proximity; (h)coalescing the paired first and second sample droplets as the paireddroplets pass through an electric field, and (i) detecting enzymeactivity within the coalesced droplets, wherein the conversion ofsubstrate to product indicates the presence of an enzyme library.

In a small library, the use of microfluidic system to emulsify a libraryof 3-5 bacteria strains that encode a single protease with a known rangeof activity against a designated substrate in microdroplets, and sortvia a fluorescence assay to demonstrate the ability to identify and sortone of the cell strains that expresses a protease that is more activeagainst a specified substrate than the other strains.

Further in a full library screen, the use of a microfluidic system toemulsify a library of mutagenized bacteria cells in microdroplets,identify and sort via a fluorescence assay a subpopulation of cells toproduce a 10⁴ fold enrichment of cells expressing a designated enzymevariant, and recover viable cells and enriched library.

The present invention provides a method for sorting a plurality ofcells, comprising (a) providing a first sample fluid wherein said firstsample fluid comprises an emulsion library comprising a plurality ofaqueous droplets within an immiscible fluorocarbon oil comprising atleast one fluorosurfactant, said droplets comprising at least one celllabeled with an enzyme; (b) providing a second sample fluid wherein saidsecond sample fluid comprises a plurality of aqueous droplets within animmiscible fluorocarbon oil comprising at least one fluorosurfactant,said droplets comprising at least one substrate; (c) providing amicrofluidic substrate comprising at least two inlet channels adapted tocarry at least two dispersed phase sample fluids and at least one mainchannel adapted to carry at least one continuous phase fluid; (d)flowing the first sample fluid through a first inlet channel which is influid communication with said main channel at a junction, wherein saidjunction comprises a first fluidic nozzle designed for flow focusingsuch that said first sample fluid forms a plurality of droplets of afirst uniform size in said continuous phase; (e) flowing the secondsample fluid through a second inlet channel which is in fluidcommunication with said main channel at a junction, wherein saidjunction comprises a second fluidic nozzle designed for flow focusingsuch that said second sample fluid forms a plurality of droplets of asecond uniform size in said continuous phase, wherein the size of thedroplets of the second sample fluid are smaller than the size of thedroplets of the first sample fluid; (f) providing a flow and dropletformation rate of the first and second sample fluids wherein thedroplets are interdigitized such that a first sample fluid droplet isfollowed by and paired with a second sample fluid droplet; (g) providingchannel dimensions such that the paired first sample fluid and thesecond sample fluid droplet are brought into proximity; (h) coalescingthe paired first and second sample droplets as the paired droplets passthrough an electric field; (i) detecting enzyme activity within thecoalesced droplets, and (j) selecting cells where the enzyme hasconverted substrate to product.

Whole Genome Amplification

Whole Genome Amplification (WGA) is a method that amplifies genomicmaterial from minute samples, even from a single cell, enabling genomesequencing. A number of commercially available WGA methodologies havebeen developed, including PCR-based methods like degenerateoligonucleotide primed PCR (DOP-PCR) and primer extensionpre-amplification (PEP-PCR), and multiple displacement amplification(MDA) which uses random hexamers and using high fidelity D29 or Bst DNApolymerases to provide isothermal amplification. Several analyses haveshown that MDA products generate the least amplification bias andproduce a higher yield of amplified DNA. This method has been usedrecently to amplify genomic DNA for sequencing from single cells, withpartial genome sequencing demonstrated. MDA-based WGA has also beenperformed on cell populations selected using flow-FISH.

Non-specific DNA synthesis due to contaminating DNA and non-templateamplification (NTA) are characteristic problems associated with WGA.Recent evidence demonstrates that NTA and also amplification bias arereduced when using very small reaction volumes, with one group using 60nanoliter microfluidic chambers for single cell WGA reactions. Based onthese findings, the use of picoliter-volume droplets in a microfluidicsystem reduces NTA even further. In addition, amplification fromcontaminating DNA templates will be constrained to individualcompartments (droplets), minimizing the overwhelming effects ofcontamination in bulk WGA reactions.

Next Generation Sequencing

Next generation sequencing instruments offer two distinct advantages inthe pursuit of microbiome characterization. First, they do not requireconventional clone-based approaches to DNA sequencing, and thus ensurethat the commonly experienced biasing against specific sequences in theE. coli host system does not impact the representation of genomes beingsequenced. Second, they offer a streamlined and robust workflow forpreparing DNA for sequencing that has far fewer steps than conventionalworkflows. Hence, a library can be prepared for sequencing in about 2days. The Roche/454 FLX pyrosequencer was the first “next generation”,massively parallel sequencer to achieve commercial introduction (in2004) and uses a sequencing reaction type known as “pyrosequencing” toread out nucleotide sequences. In pyrosequencing, each incorporation ofa nucleotide by DNA polymerase results in the release of pyrophosphate,which initiates a series of downstream reactions that ultimately producelight by the firefly enzyme luciferase. The light amount produced isproportional to the number of nucleotides incorporated (up to the pointof detector saturation). In the Roche/454 instrument, the DNA fragmentsto be sequenced first have specific A and B adapter oligos ligated totheir ends, and then are mixed with a population of agarose beads whosesurfaces carry oligonucleotides complementary to 454-specific adaptersequences on the DNA fragments, such that each bead is associated with asingle DNA fragment. By isolating each of these fragment:bead complexesinto individual oil:water micelles that also contain PCR reactants,thermal cycling (“emulsion PCR”) of the micelles produces approximatelyone million copies of each DNA fragment on the surface of each bead.These amplified single molecules are then sequenced en masse by firstarraying them into a PicoTiter Plate (PTP—a fused silica capillarystructure), that holds a single bead in each of several hundred thousandsingle wells, providing a fixed location at which each sequencingreaction can be monitored. Enzyme-containing beads that catalyze thedownstream pyrosequencing reaction steps then are added to the PTP, andcentrifuged to surround the agarose beads. On instrument, the PTP actsas a flow cell, into which each pure nucleotide solution is introducedin a stepwise fashion, with an imaging step after each nucleotideincorporation step. Because the PTP is seated opposite a CCD camera, thelight emitted at each bead that is being actively sequenced is recorded.In practice, the first four nucleotides (TCGA) on the adapter fragmentadjacent to the sequencing primer added in library construction arefirst to be sequenced, and this sequence corresponds to the sequentialflow of nucleotides into the flow cell. This strategy allows the 454base calling software to calibrate the light emitted by a singlenucleotide incorporation, which then enables the software to call novelbases downstream according to the light emission levels. However, thecalibrated base calling cannot properly interpret long stretches (>6) ofthe same nucleotides occurring in a stretch (“homopolymer” run), due todetector saturation, so these stretches are prone to base insertion anddeletion errors during base calling. By contrast, since eachincorporation step is nucleotide specific, substitution errors arerarely encountered in Roche/454 sequence reads.

Enzyme Inhibitor Screening

The present invention provides a method for screening for an enzymeinhibitor, comprising (a) providing a first sample fluid wherein saidfirst sample fluid comprises an emulsion library comprising a pluralityof aqueous droplets within an immiscible fluorocarbon oil comprising atleast one fluorosurfactant, said droplets comprising at least onecompound; (b) providing a second sample fluid wherein said second samplefluid comprises a plurality of aqueous droplets within an immisciblefluorocarbon oil comprising at least one fluorosurfactant, said dropletscomprising at least one enzyme and substrate; (c) providing amicrofluidic substrate comprising at least two inlet channels adapted tocarry at least two dispersed phase sample fluids and at least one mainchannel adapted to carry at least one continuous phase fluid; (d)flowing the first sample fluid through a first inlet channel which is influid communication with said main channel at a junction, wherein saidjunction comprises a first fluidic nozzle designed for flow focusingsuch that said first sample fluid forms a plurality of droplets of afirst uniform size in said continuous phase; (e) flowing the secondsample fluid through a second inlet channel which is in fluidcommunication with said main channel at a junction, wherein saidjunction comprises a second fluidic nozzle designed for flow focusingsuch that said second sample fluid forms a plurality of droplets of asecond uniform size in said continuous phase, wherein the size of thedroplets of the second sample fluid are smaller than the size of thedroplets of the first sample fluid; (f) providing a flow and dropletformation rate of the first and second sample fluids wherein thedroplets are interdigitized such that a first sample fluid droplet isfollowed by and paired with a second sample fluid droplet; (g) providingchannel dimensions such that the paired first sample fluid and thesecond sample fluid droplet are brought into proximity; (h) coalescingthe paired first and second sample droplets as the paired droplets passthrough an electric field, and (i) detecting enzyme activity within thecoalesced droplets, wherein the failure of the enzyme to convert thesubstrate to product indicates the compound is an enzyme inhibitor.

The present invention provides compositions and methods for generating,manipulating, and analyzing aqueous droplets of precisely defined sizeand composition. These microfluidic device-generated droplets canencapsulate a wide variety of components, including those that are usedin enzymatic assays. Kinases are a therapeutically important class ofenzymes, and this collaboration examines the feasibility of performinganalysis and interrogation of kinases with potentially inhibitorycompounds using the described microfluidic platform and systems.

High-Throughput Droplet Live-Dead Assay Screening

The present invention provides a method for screening for a live cell,comprising (a) providing a first sample fluid wherein said first samplefluid comprises an emulsion library comprising a plurality of aqueousdroplets within an immiscible fluorocarbon oil comprising at least onefluorosurfactant, said droplets comprising at least one cell; (b)providing a second sample fluid wherein said second sample fluidcomprises a plurality of aqueous droplets within an immisciblefluorocarbon oil comprising at least one fluorosurfactant, said dropletscomprising at least one cell-membrane-permeable fluorescent dye and atleast one cell-membrane-impermeable fluorescent dye; (c) providing amicrofluidic substrate comprising at least two inlet channels adapted tocarry at least two dispersed phase sample fluids and at least one mainchannel adapted to carry at least one continuous phase fluid; (d)flowing the first sample fluid through a first inlet channel which is influid communication with said main channel at a junction, wherein saidjunction comprises a first fluidic nozzle designed for flow focusingsuch that said first sample fluid forms a plurality of droplets of afirst uniform size in said continuous phase; (e) flowing the secondsample fluid through a second inlet channel which is in fluidcommunication with said main channel at a junction, wherein saidjunction comprises a second fluidic nozzle designed for flow focusingsuch that said second sample fluid forms a plurality of droplets of asecond uniform size in said continuous phase, wherein the size of thedroplets of the second sample fluid are smaller than the size of thedroplets of the first sample fluid; (f) providing a flow and dropletformation rate of the first and second sample fluids wherein thedroplets are interdigitized such that a first sample fluid droplet isfollowed by and paired with a second sample fluid droplet; (g) providingchannel dimensions such that the paired first sample fluid and thesecond sample fluid droplet are brought into proximity; (h) coalescingthe paired first and second sample droplets as the paired droplets passthrough an electric field, and (i) detecting fluorescence within thecoalesced droplets, wherein the detection of fluorescence ofcell-membrane-permeable dye indicates a droplet comprising a dead celland the detection of fluorescence of cell-membrane-impermeable dyeindicates a droplet comprising a live cell.

Single-cell analysis in the context of cell populations avoids the lossof information on cellular systems that is inherent with averagedanalysis. In recent years, this type of analysis has been aided by thedevelopment of sophisticated instrumentation. Microfluidic technologieshave the potential to enhance the precision and throughput of thesesingle-cell assays by integrating and automating the cell handling,processing, and analysis steps. However, major limitations inmicrofluidic systems hinder the development of high-throughput screeningplatforms. One challenge is to achieve sufficiently short mixing times.Mixing under the laminar flow conditions typically found in microfluidicdevices occurs by diffusion, a relatively slow process for biologicalmaterial and biochemical reactants. Most importantly, as the scale ofthese reactors shrinks, contamination effects due to surface adsorptionand diffusion limit both the smallest sample size and the repeated useof channels for screening different conditions. These limitations aremajor hurdles when this technology is to be applied for screeninglibraries containing thousands of different compounds each correspondingto different experimental conditions.

The confinement of reagents in droplets in an immiscible carrier fluidovercomes these limitations. The droplet technology is an essentialenabling technology for a high-throughput microfluidic screeningplatform. Droplet isolation allows the cells to be exposed to discreteconcentrations of chemicals or factors. Most importantly, the dropletformat ensures that the sample materials never touch the walls of themicrofluidic channels and thus eliminates the risk of contamination. Thereagents can be mixed within a droplet and sample dispersion issimultaneously minimized. The advantages of this technique include thephysical and chemical isolation of droplets from one another and theability to digitally manipulate these droplets at very high-throughput.Finally, the absence of any moving parts and in particular valves bringsthe degree of robustness required for screening applications.

Possible cell applications include screen for combinatorial cell assays,cloning, FACS-like assays, and polymer encapsulation for cell-basedtherapies. As a small number of cells are consumed per sample, thistechnology is particularly suitable for working with cells of limitedavailability, like primary cells. In addition, for rare cell sorting,the dilution factor in the collection droplets can be orders ofmagnitude smaller than for a standard bench-scale flow cytometer.Finally, the use of fluorocarbons that can dissolve large amount ofoxygen as carrier fluids is regarded as a key feature for long-termsurvival of encapsulated cells.

Numerous modules have been developed for performing a variety of keytasks on droplets. They include the generation of monodisperse aqueousdroplets and its use for cell encapsulation. Droplets can be fused orcoalesced, their content mixed, incubated on-chip, and their incubationtime tuned with an oil-extractor, their fluorescent content can beinterrogated, and finally they can be sorted. The assembly of suchmodules into complete systems provides a convenient and robust way toconstruct droplet microfluidic devices that would fulfill the promisesof the droplet technology as a screening platform.

Example 9 illustrates some examples of live-dead assays. The device hasbeen designed to sequentially accomplish six different functions: (i)separated cell and dye encapsulations, (ii) fusion of dropletscontaining cells and droplets containing dyes, (iii) mixing of cell withdyes in each fused droplet, (iv) oil-extraction to modulate on-chipincubation of droplets, (v) droplet incubation on-chip and (vi)interrogation of the fluorescent signal of each droplet. Furthermore,encapsulated cells can be collected into a syringe and re-inject theemulsion for on-chip scoring.

Kits

As a matter of convenience, predetermined amounts of the reagents,compound libraries, and/or emulsions described herein and employed inthe present invention can be optionally provided in a kit in packagedcombination to facilitate the application of the various assays andmethods described herein. Such kits also typically include instructionsfor carrying out the subject assay, and may optionally include the fluidreceptacle, e.g., the cuvette, multiwell plate, microfluidic device,etc. in which the reaction is to be carried out.

Typically, reagents included within the kit are uniquely labeledemulsions containing tissues, cells, particles, proteins, antibodies,amino acids, nucleotides, small molecules, substrates, and/orpharmaceuticals. These reagents may be provided in pre-measuredcontainer (e.g., vials or ampoules) which are co-packaged in a singlebox, pouch or the like that is ready for use. The container holding thereagents can be configured so as to readily attach to the fluidreceptacle of the device in which the reaction is to be carried out(e.g., the inlet module of the microfluidic device as described herein).In one embodiment, the kit can include an RNAi kit. In anotherembodiment, the kit can include a chemical synthesis kit. It will beappreciated by persons of ordinary skill in the art that theseembodiments are merely illustrative and that other kits are also withinthe scope of the present invention.

Enzyme Quantification

Described herein are methods for counting enzyme molecules in fluidpartitions such as, for example, microdroplets. A number of readoutmodes and multiplexing formats are illustrated, and examples of assayscoupled to the digital readout are shown.

In some embodiments, methods of the invention include a sandwichimmunoassay, allowing for absolute counting of protein molecules in asample (digital droplet ELISA). Any upfront assay that uses a chemicalreaction at least one component of which includes a detectable label(e.g., a reporter enzyme system) can be used. Any suitable detectablelabel may be included (e.g., a fluorescent product, or other optical ordetectable non-optical product) can be used with methods of theinvention.

In certain embodiments, the invention provides methods for the directdetection and quantification of enzymatically active moleculespotentially contained in samples (e.g., “bio-prospecting”). Reportersubstrates specific for the target enzyme or enzyme class are used toassay for enzyme-containing samples (or coupled enzyme and substratesreport to report on another enzyme molecule). For example, a sample canbe obtained that is suspected to contain a target molecule of interestor a target molecule member of a class of interest. The sample can bedistributed into a plurality of fluid partitions. Further, where aspecific activity or moiety is of interest or if enzymes having a rangeor threshold of specific activity are of interest, a large number oftargets can be assayed using methods and systems of the invention. Thetargets can be distributed among a plurality of fluid partitions, andeach partition can be provided with reagents for a certainenzyme-catalyzed reaction. The occurrence of the reaction in certainpartitions can be detected. Optionally, using sorting methods,enzyme-positive partitions can be isolated for further analysis. Thus, asingle (or very low amount of) target, even an unknown target, can beidentified and isolated according to activity. Further discussion can befound in Miller, et al., PNAS 109(2):378-383 (2012); Kiss, et al., Anal.Chem. 80(23):8975-8981 (2008); and Brouzes, et al., Droplet microfluidictechnology for single-cell high-throughput screening,10.1073/PNAS.0903542106 (Jul. 15, 2009), the contents of which arehereby incorporated by reference in their entirety.

Methods of the invention allow for the detection of two or more enzymemolecules or other molecules in a complex that can be assayed using anenzymatic reporter or other activatable and readable reporter (e.g.protein aggregation assay for mis-folded or disease associatedmolecules). Methods include providing separately detectable substratesfor each enzyme species or where complexes/aggregates are detected bydifferent product concentrations using the same enzyme type. A complexcan be detected as both product signals are detected in the same fluidpartition even when the fractional occupancy is low. For example, atvery low fractional occupancies, there is a vanishing probability of thetwo enzymes being found in some number of the same fluid partitions ifnot in a complex together (modeled according to Poisson statistics).Thus, the detection of both product signals reveals a protein-proteininteraction between the two enzymes.

A number of examples are shown utilizing ‘endpoint’ type digitalcounting, where the enzymatic reaction has reached a plateau. More thanone endpoint can also be used for detection of multiple species. Theinvention further includes measurements at earlier time points duringthe reaction (‘kinetic’ measurements vs. ‘endpoint’ measurements) suchthat different signal intensities from single enzyme molecules reflectdifferences in enzymatic specific activity, the presence of inhibitoryor activating molecules, or the presence of more than one enzymemolecule per droplet. Kinetic mode measurements can be made followingdroplet incubation at the appropriate temperature either off chip or onchip. For on-chip measurements, a ‘timing module’, such as a delay line,can be used to keep droplets on-chip for an appropriate length of time,and one or multiple measurement points along the length of themicrofluidic channel can enable very precise kinetic measurements. Adelay line can include, for example, a channel in a chip through whichdroplets flow. A delay line may include locations for stopping droplets,or locations for moving droplets out of the may stream of flow, orlocations for droplets to separate from the oil by buoyancy differencesbetween the oil and the droplets. A delay line may include a means ofadding or removing oil to speed up or slow down the rate of travel ofdroplets through the delay line. A delay line may include neck-downs orother features to homogenize the average velocity of the droplets andminimize dispersion effects as droplets travel through the channel. Adroplet trap may be utilized to trap droplets for a fixed period of timebefore releasing the droplets. Such a trap may include a valve, orrequire the reversal of the direction of flow through the trap region torelease the trapped droplets or it may require that the chip be flippedover to reverse the direction that the droplets move in thegravitational field. One skilled in the art will recognize a number ofways to control the timing of the reaction. A portion of the channel mayhave a much broader cross-sectional area that upstream or downstreamportions. Thus, for a certain volume per time flow rate, the distanceper time flow rate in the broad portion will be much slower. Workingwith fluidic chips and known droplet behaviors, a channel can bedesigned with a delay line that delays the flow for a predeterminedamount of time. This can allow reactions to incubate or progress for theappropriate amount of time. Temperature control of specific regions maybe included in chip designs and interfaces with the chips.

Analyte or reporter molecule may also include non-enzyme species,provided the molecule or complex participates in generation of areadable signal (e.g. an enzymatic activator or inhibitor).

In general, the invention provides methods and systems for measuring amolecular target. A plurality of fluid partitions are formed. Fluidpartitions can be any known in the art such as, for example, wells on aplate or water-in-oil droplets. A detectable reaction, such as anenzyme-catalyzed reaction, is performed in some subset of the fluidpartitions. For example, where a sample suspected of containing themolecular target is separated into the fluid partitions (including viaan optional dilution or serial dilution step), the subset of partitionsthat contain the target will include a certain number of partitions.That number can be associated with the amount of target in the sample.

A detectable reaction occurs in the subset of partitions that containthe molecular target. In some embodiments, the molecular target is anenzyme, and all of the partitions are provided with a fluorescentlylabeled substrate. The enzyme-catalyzed reaction can release thefluorescent label from the substrate such that the fluor becomesun-quenched or can be quantified by its location in the partition. Incertain embodiments, the target is a substrate, and all of thepartitions are provided with an enzyme and optionally an additionalsubstrate or a co-factor. One of the reaction ingredients contains amolecular label that is released when the reaction occurs.

Because a productive reaction only takes place within the subset ofpartitions that contain the target, determining the number of partitionswithin which the reaction takes place (i.e., determining the number ofthe subset) allows one to determine the amount of target in the originalsample. Since each partition is counted as reaction-positive orreaction-negative (e.g., in the subset or not), this detection is saidto be digital. This includes cases where the positives can be furtherquantified as containing quantized numbers of targets.

In certain embodiments, digital detection operates through a reactionthat includes a number of stages including, in various embodiments,enzymes that are themselves substrates for other enzyme-catalyzedreactions and substrates and/or enzymes or targets that are dark (i.e.,not reporting) when participating in reactions and that are detectablewhen not. To illustrate, in certain embodiments, a partition includes anenzyme and a substrate which together will report the presence andnumber of target molecules. The substrate is labeled such that it givesa dark state as long as the enzyme is present. A target molecule thatinhibits the enzyme can be assayed for according to the steps describedherein. Since the target inhibits the reporting enzyme, then presence ofthe target will cause the reporter to generate a readable signal.

In certain embodiments, a substrate is included in a reaction mixturealong with an enzyme that catalyzes a readable reaction of thesubstrate, but the included enzyme is in an inactive form and exposureof the included enzyme to the target molecule will catalyze itsconversion to an active form. In this fashion, the presence or absenceof target initiates an enzyme cascade that results in a readable assay(the cascade can include multiple steps) and quantified. In oneembodiment, an apoenzyme is used to detect the presence of a protease.The apoenzyme is provided in a fluid partition with a substrate of theactive form of the enzyme. The apoenzyme will only be cleaved to formthe active form if the protease is present in the target sample.

The invention further provides methods and systems for detecting orquantifying the presence of an enzyme inhibitor or activator. Forexample, fluid partitions can be provided with an enzyme and itssubstrate. A sample suspected to contain an inhibitor or activator isseparated into the partitions (with optional dilution). Release of areporter via an enzyme catalyzed activity indicates the presence of anactivator or absence of an inhibitor. Further, enzyme kinetics as wellas inhibition or activation can be studied with methods describedherein.

Methods of the invention can be used with any suitable enzyme(s) orsubstrate(s). For example, beyond the variety of examples given herein,the invention can further be used to detect cleavage of a peptide by aprotease. Where a sample is suspected to contain a protease, afluorescently labeled peptide substrate can be provided in the fluidpartitions.

As another example, methods of the invention can include use of apolymerase enzyme and fluorescently labeled nucleotides to detectactivity of a ligase. Given the appropriate conditions, the polymerasewill only act on a product of a reaction catalyzed by the ligase (e.g.,a polynucleotide). When the polymerase catalyzes a reaction it releasesthe fluorescent reporter as a readable signal.

In one other illustrative example, the presence, type, and number ofrestriction enzyme(s) can be quantified by providing a construct thatincludes an oligonucleotide with a fluor and a quencher close enough toeach other that the quencher quenches the fluor but is separated by arestriction site. The presence of the restriction enzyme in the targetsample will light up what is otherwise a dark fluid partition. Thepresence, type, and number of a set of analytes can be assayed usingrestriction enzymes that are specific for different readable substrates,or can be configured into a ‘one-of-many’ type of assay where all theanalytes have the same restriction enzyme and substrate, or can begrouped into different classes using enzyme/substrate classes.

In certain embodiments, the invention provides systems and methods fordetecting and quantifying classes of enzymes or substrates. Any class oftarget can be the subject of an assay including, for example, allenzymes exhibiting a certain activity or all enzymes in a certaintaxonomic group.

Another embodiment includes a downstream reporter that is split (e.g.,split green fluorescent protein or a split enzyme reporter) intomultiple parts that do not interact productively in the absence of theupstream reporter (e.g. cleavage of the modified downstream reporter bythe upstream reporter enzyme-oligo-modified reporter activated by theaction of a restriction enzyme or a peptide-modified reporter activatedby protease reporter), or that require being brought into closeproximity for activity (e.g. following cleavage of the inhibitingmodification, two halves of a split enzyme are brought into proximityfor folding and activation). Two subsections of the reporter can beseparated by an oligo containing a restriction site such that if therestriction enzyme (or, remembering that an enzyme can in turn be asubstrate for another enzyme, an enzyme that activates the restrictionenzyme) is present, the oligo is cleaved and the two subsections cancome together to form the active reporter. Alternatively, cleavage oflinked moieties can release inhibition of an activity that produces areadable signal.

One of skill in the art will recognize that any number of the examplesgiven herein can be combined to create multi-step assays. Thus, forexample, a restriction enzyme can cleave an oligo that is separating twohalves of a protease. The active protease can cleave an apoenzyme torelease an active phosphorylase that phosphorylates and de-activates adownstream enzyme. If the downstream enzyme is an inhibitor of a finalenzyme, then deactivation of a downstream enzyme can result in activityof the final enzyme. One of skill in the art will recognize the widevariety of combinations of the scenarios given herein that can be used.

FIGS. 8A-8G show a workflow example for a digital droplet reporterenzyme assay. In FIG. 8A, the enzyme molecules to be counted are mixedwith a fluorogenic substrate and loaded into droplets via introductioninto a microfluidic nozzle. The aqueous mixture of enzyme and substrateflows down inlet channel 101 and forms an emulsion when merged with oilfrom carrier fluid channels 103 a and 103 b. In FIG. 8A, arrows indicatethe direction of flow. The co-infusion of an immiscible oil segments theaqueous stream into a number of uniformly sized droplet 109.

The droplet emulsion is collected into a suitable container for off-chipincubation at an appropriate temperature for enzymatic function.

FIG. 8B illustrates a schematic overview of a reaction according tocertain embodiments of the invention. In general, as shown in FIG. 8B,an enzyme 113 catalyzes the conversion of a fluorogenic substrate 111 toa fluorescent product 115.

In one exemplary embodiment, enzyme 113 was streptavidin-conjugated betagalactosidase (β-gal) (Calbiochem product #569404 from Merck KGaA(Darmstadt, Germany)) and fluorogenic substrate 111 was fluoresceindi-β-D-galactopyranoside (FDG) sold under the trademark MOLECULAR PROBESas product number F1179 by Life Technologies (Carlsbad, Calif.), withactive enzyme able to cleave the substrate to release, as fluorescentproduct 115, fluorescein isothiocyanate (FITC) and two galactose.

As shown in FIG. 8C, after incubation of the droplet emulsion at 37° C.for a determined time, the droplet temperature can be changed such thatthe enzyme is no longer affecting the readable signal, and the dropletscan be infused into a second microfluidic nozzle 117, spaced into atrain of individual droplets using an immiscible oil, and run past laserspot 119 focused in microfluidic channel 121. FIG. 8D is an illustrationdepicting the detection step when no enzyme is present (or after enzymeis loaded but before incubation). The droplets in FIG. 8D all exhibituniformly low fluorescence intensity, indicating a lack of conversion ofsubstrate 111 to product 115.

As discussed with reference to FIGS. 8C-8E, detection can includedroplets flowing past a detector. However, any suitable method ofdetecting an enzymatic reaction in a fluid partition can be usedincluding, for example, optical or non-optical detection such as pHchange or change in impedance or conductivity within a fluid partition,or any other suitable detection method. In some embodiments, non-opticaldetection includes nuclear magnetic resonance (NMR) analysis ofmaterials from fluid partitions. Detection after release of thedigitally generated reporter moieties from the partitions may also beused (e.g. array, electrode, magnet, sequencer, mass spectrometer, othermethods).

FIG. 8E is an illustration depicting the detection step when a lowconcentration of enzyme is present, after incubation. Laser spot 119 isused to detect a number n of positive droplets 125 a, 125 b, . . . , 125n. By counting the results of laser detection, the number of partitions(here, droplets) in the subset of partitions in which anenzyme-catalyzed reaction occurred is determined.

The resulting signal time traces from detection photomultiplier tubesshow examples for when either there were no enzyme molecules loaded orafter loading enzyme molecules but before incubation (shown in FIG. 8Fwith an insert showing a zoomed image of 10 individual droplet traces),and droplets generated with a low concentration of enzyme afterincubation (FIG. 8G). The droplets that have no enzyme molecules (orhave enzyme molecules that were not incubated to allow for enzymaticactivity) show uniformly low fluorescent signal intensity, coming fromthe unconverted fluorogenic substrate. For the case where a lowconcentration of enzyme was used (see FIG. 8G) loading of enzymemolecules into droplets occurs in a quantized manner, with the signaltime trace showing droplets that have no enzyme molecules (with similarsignal intensity to that seen at generation) and droplets with enzymemolecules (showing quantized levels of signal intensity that correspondto different numbers of enzyme molecules per droplet).

The distribution of the number of enzyme molecules per droplet (i.e. 0,1, 2, 3, etc. molecules per droplet) is dependent on the startingconcentration of enzyme loaded into the droplets and the whether theenzyme molecules are in un-dissociated complexes. FIGS. 9A-9D and FIGS.10A-10D illustrate this phenomenon, showing the time traces (FIGS.9A-9D) and histogram distributions (FIGS. 10A-10D) for increasingconcentrations of β-gal, as shown by fluorescent intensity of FITC(lowest concentration shown in FIGS. 9A and 10A, highest concentrationshown in FIGS. 9D and 10D). These measurements were made on dropletsthat had been incubated for about an hour. As the starting enzymeconcentration is increased, the time traces show the number of‘negative’ (no enzyme) droplets decrease, the number of ‘positive’droplets increase, and the number of enzyme molecules in any positivedroplet increases (seen as a higher signal intensity).

The distribution of enzyme molecules into droplets can occur accordingto a Poisson Distribution, or can occur in a non-Poisson fashion. FIG.10A shows a non-Poisson distribution. In some cases the degree to whichthe distribution varies from a Poisson distribution will be indicativeof a degree of aggregation of the component. In some cases theinterpretation of the variation from a Poisson distribution will bediagnostic. In FIG. 10A, the x-axis is given in volts indicting reporterintensity as measured through a photomultiplier. An appropriate scalingfactor can be used (e.g., determined separately) to convert V to numberof molecules per droplet. As shown in FIG. 10A, the first peak at about0.1 V can indicate that a number of the droplets (i.e., Drop Count) thathad no s-gal activity in them. The second peak about 0.23 V can indicatea number of droplets that each had one active unit of enzyme. The thirdpeak about 0.42 V can indicate a number of droplets that each containedtwo active units of enzyme. The fourth peak, at about 0.58 V, canindicate a number of droplets that contained three units of activeenzyme. The fifth peak, at about 0.76 V, can indicate a number ofdroplets that contained four active units of enzyme. FIGS. 10B-10C showgreater concentration of enzyme (i.e., less dilution). In certainembodiments, for an enzyme that exhibits no aggregation or covalent ornon-covalent complex formation, a plot at the concentration illustratedin FIG. 10A would show a Poisson distribution. FIG. 10A can indicatethat a substantial and statistically significant number of dropletscontain more than 1 enzyme unit than is predicted by Poisson. Thus, FIG.10A can show that β-gal exhibits aggregation. When the starting enzymeconcentration is 1.6 pM (FIGS. 9D and 10D, there are no negativedroplets, and the histogram shows most droplet signals centered around asingle mean value, with a much smaller number showing a quantizeddistribution like that seen at lower concentrations (several small peaksclose to the origin).

FIGS. 11A and 11B show an example of how this data can be used toquantify the concentration of active enzyme molecules loaded intodroplets. FIG. 4A shows a readout histogram from an enzyme concentrationthat was calculated to be 0.0128 pM. Using the histogram from an enzymeconcentration calculated to be 0.0128 pM, based on multiplying thestarting concentration and the dilution factor (FIG. 11A), each peak'smean is determined and plotted as a function of integer enzyme moleculesto show linearity (FIG. 11B). The number of droplets within each peakand the number of active enzyme molecules within each peak are countedand tabulated. The results are listed in Table 1.

TABLE 1 Distribution of #Droplets with #Molecules Enzyme/dropletDroplets #enzymes 0 113458 0 1 15249 15249 2 3637 7274 3 1356 4068 4 5362144 5 280 1400 6 139 834 7 73 511 >7 138 1405 Total: 137866 32885

By dividing the totals from Table (number of active enzyme moleculesover total number of droplets counted) a number of molecules per dropletcan be calculated as shown in Equation 1.(#molecules/droplet)=(32885/134866)=0.24  (1)

By multiplying by the appropriate scaling factors, the measuredconcentration (MC) can be calculated using Equation 2:

$\begin{matrix}{{{MC}({pM})} = {\frac{\#\mspace{14mu}{molecules}}{droplet} \times \frac{droplet}{{volume}\mspace{14mu}({pL})} \times \frac{1.0\mspace{14mu}{pM}}{\frac{0.6023\mspace{14mu}{molecules}}{pL}}}} & (2)\end{matrix}$

Using the value given by Equation 1 in Equation 2, gives the resultshown in Equation 3.

$\begin{matrix}{{{MC}({pM})} = {{\frac{0.24\mspace{14mu}{molecules}}{droplet} \times \frac{droplet}{30\mspace{14mu}{pL}} \times \frac{1.0\mspace{14mu}{pM}}{\frac{0.6023\mspace{14mu}{molecules}}{pL}}} = {0.01275\mspace{14mu}{pM}}}} & (3)\end{matrix}$

For this example, the measured concentration was 0.01275 pM, with theexpected concentration based on dilution factor being 0.0128 pM.

The dynamic range of the assay can span regimes where the number ofenzyme molecules is discretely quantized in all droplets or where themajority of droplets (or all droplets) contain a mean (with adistribution around the mean) number of enzyme molecules. For thespecific format described in the example (i.e. droplet size, enzyme andsubstrate used) typically enzyme concentrations greater than ˜pM can beanalyzed using the mean distribution (and also the small quantized tailseen near the origin of the graph shown in FIG. 10D) and enzymeconcentrations lower than ˜pM can be analyzed using digital counting ofthe total number of droplets, the number of enzyme-containing droplets,and using the quantized signals from enzyme-containing droplets to countthe number of enzyme molecules per droplet. Thus, the dynamic range ofthe assay is extremely wide, with the lower limit of detectiondetermined by the number of detectable molecules present in the sampleand the length of time required to run a sufficient number of dropletsthrough the detector (e.g. if the droplet system runs at 10⁶ dropletsper hour, the limit of detection is 1 in 10⁶ in an hour, and the limitof detection is 1 in 10⁷ in 10 hours), and the upper limit determined bythe amount of substrate converted to product (as enzyme concentrationsget higher, the substrate concentration will have to increase in orderfor the product fluorescence to remain linearly (or correlatively)related to enzyme mean concentration). Additional parameters that can beadjusted include the time and temperature of incubation, as well as thedroplet volume used, and additional reaction components. In certainembodiments, fluid partitions are droplets and assays are performed insystems in which droplets are run past a detector at 3,000 s. In someembodiments, droplets are run at 10,000/s or at about 100,000 persecond. In some embodiments, a lower limit of detection is 1 in 10⁹ anda flow rate is 10⁹ per hour.

FIG. 12 shows an illustration of the concept and workflow for a digitaldroplet ELISA assay, one example of an upfront assay that can be coupledto the digital reporter enzyme assay readout. When proteinconcentrations are too low for standard detection methods (typicallylow-sub-picomolar), this invention enables protein quantification bycounting individual protein molecules with a fluorescent readout.Droplets containing a single molecule (e.g. in an ELISA sandwich) willbe fluorescent, and the number of fluorescent droplets in a populationof total droplets will yield a digital count of molecules per volume(i.e. concentration) down to a limit of detection dependent only on thenumber of droplets examined.

FIG. 12 shows one example ELISA assay format and should not beconsidered the only or preferred format (e.g. magnetic beads could beadded following antibody binding in solution). The protein-containingsample (three proteins shown as diamonds with the rare target protein tobe counted shown as solid diamonds) is combined with the bindingreagents and incubated for a sufficient time to bind into productivecomplexes.

In the “ELISA Sandwich Formation” step, each target protein molecule isbound to two affinity reagents (each binding separate epitopes of thesame target molecule), generating an immunoaffinity “sandwich” complex.In the example shown, one of the affinity reagents (e.g. antibody) isimmobilized onto a magnetic bead while the other biotinylated antibodyis free in solution. In certain embodiments, the number of magneticbeads (with immobilized antibody) is significantly greater than thenumber of target proteins in solution, so that single target proteinsare bound by single beads. If the second antibody is used at the sametime, its concentration should be greater than the number of targetmolecules, but less than the number of immobilized antibodies.Alternatively, the second antibody can be added following the firstbinding step (ensuring that all target molecules are bound to theimmobilized antibody first).

After the target proteins are bound into sandwich complexes, themagnetic beads are retained by a magnetic field to allow removal ofunbound non-target proteins and free antibodies, and washed to removenon-specific binders. Addition of the reporter enzyme (e.g.streptavidin-beta galactosidase) results in binding to the secondbiotinylated antibody and assembly of the final ELISA sandwich, which isagain washed to remove unbound reporter enzyme. The final material (see,e.g., FIG. 13A) is re-suspended in a small volume, along with afluorogenic substrate, for processing in the digital droplet readout.

FIGS. 13A-13D show a number of different readout ‘modes’ for running thedigital droplet readout, following the ELISA sandwich complexconstruction. In FIG. 13A, more than one magnetic bead is in eachgenerated droplet, but only a single ELISA sandwich is in any singledroplet (e.g. in this case sub-micron magnetic beads are used).

FIG. 13B shows a mode where at most a single bead is in each droplet,with at most one ELISA sandwich.

FIG. 13C shows a mode where the second antibody complexed to thereporter enzyme has been eluted off of the magnetic bead, and thedroplets are loaded such that at most one antibody-reporter complex ispresent in any droplet.

In FIG. 13D, the reporter enzyme itself is released off of the magneticbead, with droplets loaded such that at most one enzyme molecule ispresent in any droplet.

Any suitable method can be used for releasing the enzyme from the ELISAsandwich. Exemplary methods include: 1) competition of adesthiobiotin-streptavidin interaction using biotin; 2) reduction of alinker that contains a disulfide bond; 3) enzymatic cleavage of a linkergroup. Other variations can be considered, and Poisson and non-Poissonmodels can be used to enable high occupancy loading while stillproviding quantitative counting.

With reference to FIGS. 14A and 14B, the invention provides methods formultiplexing digital droplet reporter enzyme readout. Several modes formultiplexing a digital assay are provided.

In certain embodiments, methods including generating droplets thatcontain different fluorogenic substrates and enzymes that producedifferent fluorescent products. For example, beta galactosidase and FDGproduce FITC, whereas horseradish peroxidase and Amplex Red produceresorufin. The first method uses completely separate enzyme andfluorogenic substrate pairs loaded into droplets at the same time. Forexample, beta galactosidase and FDG (FITC is the fluorescent product,with a peak emission wavelength of 518 nm) can be used to count one setof target molecules, while horseradish peroxidase and Amplex Red(Resorufin is the fluorescent product, with a peak emission wavelengthof 582 nm) can be used to simultaneously report on a second set oftarget molecules, as the detection wavelengths can be easilydistinguished with standard laser/filter setups.

Some combinations of different reporter enzymes and different substratesproducing the same fluorescent product can be used. For example, betagalactosidase catalyzes reactions of FDG while alkaline phosphatasecatalyzes reactions of FDP, with each of these combinations producingthe same fluorescent product (FITC). Nonetheless, the endpoint productconcentration for each single enzyme can be discriminated whenmultiplexing.

FIG. 14A illustrates discrimination by signal strength at endpoint.While different enzymes and substrates are used, the substrates generatethe same fluorescent product (e.g. FITC). Careful titration of theendpoint product concentrations can enable separate counting of eachtarget (e.g., traces with distinct intensities in FIG. 14A).

FIG. 14B illustrates discrimination by running at different time points.In these embodiments, a kinetic assay can be used rather than anendpoint assay (e.g. alkaline phosphatase and fluorescein diphosphateyield FITC as a product with much faster kinetics than betagalactosidase and FDG). One assay (assay #1) runs for a period of timeand produces a detectable product. After an amount of time, thedetectable product hits a plateau in intensity. Assay #1 is multiplexedwith (i.e., run simultaneously with) assay #2. Assay #2 proceeds moreslowly than assay #1. By the time that assay #2 begins any substantiallyuptick in activity, the product of assay #1 has plateaued. Thus, thelevel of detectable product from the plateau of assay #1 provides abaseline for the level of product of assay #2. Such a pattern can befurther multiplexed to any suitable level of plexity.

In certain embodiments, all droplets within an assay have asubstantially identical size (e.g., even where optical labeling isused). The same nozzle 105 can be used to generate droplets of identicalsize (discussed in greater detail below). Further, since all dropletsare labeled separately for multiplexing, the droplets can be incubatedidentically, due to the fact that they can be handled in the samechamber or apparatus. Similarly, all droplets can be read with the sameoptical mechanism (e.g., they all flow through the same channel past thesame detection point on-chip). Thus, optical sample indexing allows forhigher throughput and better data comparisons.

While some descriptions herein illustrate digital enzyme quantificationin droplets, systems and methods of the invention are applicable to anysuitable fluid partition. Fluid volumes for partitions can be providedby chambers made from closing valves, SLIP-chips, wells, spontaneousbreakup to form droplets on a structured surface, droplets formed usingelectrowetting methods, etc.

Allele-Specific Assay

FIG. 17 shows an illustration of the concept and workflow for a digitaldroplet competitive allele specific enzyme hybridization (CASE) assay,another example of an upfront assay that can be coupled to the digitalreporter assay readout. The CASE hybridization assay usesallele-specific oligonucleotide probe hybridization to select raregenomic targets for binding to the reporter enzyme and subsequentdigital counting.

Two probe types are used. Wild-type probe 130 is complimentary to theabundant wild-type allele. Wild type probe 130 includes a minor groovebinding motif 134 (either 5′ or 3′ to the targeting oligonucleotide).

Mutant probe 131 is complimentary to the rare mutant allele. Mutantprobe 131 includes an immunoaffinity tag 135 (e.g., TAG) on one end anda biotin on the other end. Other binding motifs can be used, but in thisexample a DIG TAG (which can be bound by an anti-DIG antibody) andbiotin (which can be bound by streptavidin) are used.

Wild-type probe 130 with minor groove binder 134 out-competes anynon-specific binding of mutant probe 131 to the wild-type sample DNA,thus limiting hybridization and duplex formation such that only twoduplex species form: wild-type DNA hybridized to wild-type probe 130,and mutant DNA hybridized to mutant probe 131. An excess of the twoprobes over sample DNA is used, ensuring that each single strand ofmutant sample DNA is in a duplex with one mutant allele probe.

Following duplex formation, a single-strand nuclease is added such as Sinuclease. The nuclease digests any unbound mutant probe 131 such thattag 135 is dissociated from the biotin.

Magnetic beads coupled to anti-TAG antibodies are next added in excess,such that each bead will bind at most one complex of probe 131 and tag135. The beads are immobilized using magnet 137 and washed to removenon-specifically bound material (digested biotinylated probe and thesingle strand nuclease).

Streptavidin-coupled reporter enzyme 139 is next added. After washing,the only enzyme remaining immobilized on the magnet is present in aone-to-one stoichiometry with the original rare mutant allele present inthe sample DNA. Finally, the reporter enzyme is counted using thedigital droplet reporter enzyme assay, as above.

While shown in FIG. 17 in a certain embodiment, a CASE assay can includeany suitable probes for a particular assay. The anti-TAG antibodies canbe provided on any suitable solid substrate. Reporter enzyme 139 can beany suitable enzyme, such as any of those discussed herein.

Optical Labeling

In certain aspects, the invention provides methods and devices foroptical labeling of samples or assays. Methods of optical labelinginclude adding a dye to a sample or assay before droplet formation.Different samples or assays can be multiplexed by adding one dye atdifferent concentrations. FIG. 18A shows a plot in which the x-axiscorresponds to the droplet assay signal and the y-axis corresponds todifferent concentrations of dye. As can be seen from FIG. 18A, fluidpartitions can include dye in six different concentrations and still beclearly optically resolvable from one another. More than six differentconcentrations can be used such as, for example, seven, ten, fifty, ormore.

Optical labeling can include further multiplexing by using additionaldyes. For example, FIG. 18B shows a plot in which the x-axis shows 10different concentrations of a dye that emits at 590 nm, while the y-axisshows 10 different concentrations of day that emits at 650 nm. Byincluding two dyes at 10 concentrations each, 100 samples can beseparately labeled and run through a single assay (99 samples are shownin FIG. 18B).

Multiplexing by these methods provides a high throughput readout. Incertain embodiments, a single dye laser set allows for 6-7 or more(e.g., 10, 25, more) index levels per run. An additional laser thenallows greater numbers (e.g., >30). By multiplexing at these levels,positive and negative controls can be run in an assay.

FIG. 18C shows the high levels of “plexity” for multiplexed reactionsusing different concentrations of an optical dye and differentcombinations of fluorescently labeled antibodies. As shown in FIG. 18C,each circle represents a fluid partition. Each inverted “Y” memberrepresents an antibody. The labels “AB #1”, “AB #2”, . . . , “AB #20”refer to twenty different antibodies, and indicate that in any givenfluid partition, all of the antibodies are the same. The antibodies areshown with two different fluorescent markers at their heads. A spikymarker indicates a first color (e.g., green), while a globular markerindicates a second color (e.g., red). “Optical Dye [1]” indicates afirst dye concentration; “Optical Dye [2]” indicates a second dyeconcentration; “Optical Dye [3]” indicates a third dye concentration;and “Optical Dye [0]” indicates no dye.

Noting that in any given fluid partition in FIG. 18C all of theantibodies are the same, it can be seen that each fluid partition isnonetheless distinctly labeled by a combination of colored fluorescentmarkers and dye concentration. That is, no two partitions in one columncontain the same combination of colors of fluorescent labels. Further,two different optical dyes can be included in each fluid partition, eachseparately detectable and each separately able to be provided atdifferent concentrations. Imaging an idealized axis extending normal tothe surface of FIG. 18C, it can be appreciated that a second optical dyeprovided in 3 distinct concentrations will allow the assay to bemultiplexed with a “plexity” of 48—i.e., 48 different antibodies can beseparately and distinctly labeled.

Localized Fluorescence

FIGS. 16A and 16B relate to methods of reaction detection in fluidpartitions that employ a localized fluorescence method of detection. Inthese methods, positive (enzyme-containing) partitions are identifiedand counted using changes in the localized fluorescence of fluorescentmolecules in the partitions. In general, methods of the invention employany detection method that detects a localized concentration of a targetin a fluid partition. For example, in certain embodiments, enzymeactivity creates a binding surface for fluorescent molecules that can bemonitored by localized fluorescent readout.

In the example shown in FIG. 16A, the enzyme Src kinase (Src)phosphorylates a Src substrate peptide that is immobilized on a bead.Phosphorylation of the Src substrate peptide creates binding motifs forthe fluorescent reporter SH2-FITC. Thus, SH2-FITC binds to thebead-bound Src substrate phospho-peptide as shown in the last step ofFIG. 16A.

FIG. 16B illustrates a reaction-negative fluid partition on the leftside and a reaction-positive fluid partition on the right. Localizationof the fluorescent molecules onto the bead surface can be detected as anincreased signal on the bead surface, a decreased signal in a portion ofthe fluid partition (e.g., throughout the partition volume), or both.Many other enzymes, binding motifs, and fluorescent reporters can beused.

Any suitable method can be used to detect the pattern of localizedfluorescence within a fluid partition. For example, in certainembodiments, fluid droplets are flowed through a narrow channel thatforces the droplets to exhibit an elongated shape (as shown in FIG.16B). As the droplets pass a laser detector, reaction-negative dropletsgive a uniform low-level fluorescence intensity along their length,while reaction-positive droplets show a spike corresponding to when thebead-bound fluorescent reporter passes the laser detector. In addition,when fluors become localized onto particle(s) within the droplet (e.g.on a bead or a cell surface) there is a coordinate depletion of theinitial fluorescence in the regions of the droplet that do not containthe particle(s). Various signal processing algorithms can be used tocombine local signal increases and background signal decreases into amore robust detection method.

FIGS. 19A and 19B show a workflow for a localized fluorescence bindingassay. Cell sample 201 provides cells that are flowed into dropletgenerator 203. An optically labeled library 211 (e.g., according tomultiplexing embodiments discussed elsewhere herein) is flowed such thatdroplets from library 211 meet cell droplets from sample 201 in dropletmerger 207. Droplets leave merger 207 having optical labels and reagents(e.g., fluorescent antibody to a biomarker of interest) and incubated(not shown) and then flow past detector 211. In certain embodiments,detector 211 includes a narrow channel portion 225 as discussed below inreference to FIG. 20. Libraries are discussed in U.S. Pub. 2010/0022414,the contents of which are hereby incorporated by reference in theirentirety for all purposes.

FIG. 19B illustrates the principle of detection in detector 211. A fluidpartition at the top of FIG. 19B includes a plurality of fluorescentlylabeled antibody 215 and a cell presenting an antigen of interest. Afterincubation, the fluid partition appears as at the bottom of FIG. 19B,where it is shown containing only one concentration of fluorescentmarker 219, as all of the labeled antibody has bound to the cell.

FIG. 13 shows detection of CD45 on the surface of U937 monocytes withsystems and methods of the invention. An optically labeled antibodylibrary is flowed into the system from one input to merge with cellsfrom the other (tracing the cell path across the figure from left toright). The streams merge and the droplets combine, after which thedroplets are incubated “off chip”, as indicated by the middle panel, inwhich the droplets can be seen without a surrounding microfluidicchannel. After incubation, the droplets are flowed back onto a chip intoa channel, after which they are flowed through narrow channel portion225. Flowing through the narrow area causes the cells to elongate. Alaser detector reads across the channel in the middle of narrow portion225.

As the cells pass the laser, the detector detects fluorescence andcreates a digital trace that can be stored and analyzed on a computer.The digital trace can be viewed on a display as a graph, in which thex-axis represents time (and corresponds to the length of the droplets asthey pass the detector), and the y-axis corresponds to signal intensity(see example traces in FIGS. 21A-21C).

Throughput of the assay is adjustable and can be performed at, forexample, about 1500 droplets per second (in the illustrated example,corresponding to about 150 cells/second). Incubation time (e.g., offchip, as shown in middle panel) can be adjusted. On chip, incubation canbe adjusted by use of a delay line (i.e., wider portion of channel whereflow slows). The interior diameter of narrow portion 225 can be adjustedto tune droplet elongation. For example, interior diameter can be about10 micrometers or 15 micrometers.

In certain embodiments, localized fluorescence is used to screen forsingle-chain variable fragment (scFv) peptides in droplets. For example,a library of bacterially produced scFv's can be developed. Following aprocedure as outlined in FIG. 19A, transformed bacteria cells 201 areencapsulated and incubated at 37° C. After incubation the droplets arecombined with droplets that contain beads, antigens and a detectionantibody from library 211.

The droplet based binding assays utilize localized fluorescencedetection of scFv binding as shown in FIG. 19B. Specifically, thediffuse signal becomes bright and localized on the capture bead.

Positive droplets are detected according to a localized fluorescencemethod such as the one illustrated in FIG. 20. In order to get a readingof the droplet and fluorescent level therein, the droplet is elongatedfor detection in narrow channel portion 225 as shown in FIG. 20.

The positive droplets can then be broken and the contents recovered andsequenced. The process is able to screen for scFv's in droplets at arate of about 1×10⁶ per hour. Localized fluorescence and scFv screeningis discussed in U.S. Pub. 2010/0022414, the contents of which is herebyincorporated by reference in its entirety.

FIGS. 21A-21C illustrate single droplet traces including optical labelsin a localized fluorescence assay. Note that the trace in each of FIGS.14A-14C may be shown in a separate color for example on a singledisplay. In each figure, the axes are the same and the traces can beobtained in a single run detecting three differently colored labelssimultaneously. FIG. 21A shows a trace indicating measurement of cellviability stain. Here, calcein AM can be used, which gives a lowintensity signal until it is cleaved by esterases located only inside acell. The two spikes in FIG. 21A (at approximately 110 ms andapproximately 300 ms) indicate the second and fourth droplets,respectively, to pass the fluorescent detector. These two spikesindicate that those droplets included a viable cell.

FIG. 21B shows a signal strength of FITC signal for droplets thatinclude a labeled binder (e.g., anti-CD45-FITC). A spike (e.g., at 30ms) indicates binding (i.e., a localized increase in fluorescence) while“bulges” centered on about 60 ms, 125 ms, 190 ms, 355 ms, 420 ms, and480 ms (corresponding to the second, third, fourth, sixth, seventh, andeight droplets to flow past the detector, respectively) indicatedispersed, low-level fluorescence and thus indicate no binding. Inconjunction with to FIG. 21A, which indicate the presence of a viablecell in the fourth droplet, FIG. 21B indicates that the viable cell isbinding anti-CD45.

It will appreciated in viewing FIG. 21B that the spike at about 300 msis surrounded by a low-level “bulge” spanning about 275 ms to about 320ms. A positive assay can be detected by the low level of the signalacross this “bulge” as compared to the signal level in thereaction-negative bulges (e.g., consistently above about 0.1). Thus,localized fluorescence can be detected (and positive or negativereaction fluid partitions identified) by localized increases offluorescence, partition-wide decreases in fluorescence, or both. Forexample, a ratio could be calculated between the localized increase andthe partition-wide decrease, and this ratio would be a sensitiveindicator and/or measurement of localization within the partition.Moreover, measurement of the total volume of the partition may also betaken into consideration to further scale or normalize thepartition-wide decrease.

FIG. 21C illustrates optical labeling that was included with thedroplets shown in FIG. 14B (shown here as a blue trace). Here, controldroplets were labeled with a low concentration of dye, while testdroplets (including the anti CD45-FITC) were labeled with a highconcentration of the dye. Thus, the first three signals, the fifthsignal, and the sixth signal indicate that the corresponding fluidpartitions are negative controls. while the fourth and seventh dropletswere test partitions. An independent (e.g., downstream or upstream)channel can be used to count cells, count droplets, sort cells, orperform other steps.

FIGS. 22A-22C give single droplet traces with a scatter plot andhistogram. These figures illustrate the results of an assay for IgG andCD45. Here, two traces are superimposed. One trace indicates a level offluorescence from FITC at locations within a fluid partition (similar tothat shown in FIG. 21B). The other trace indicates a dye used indifferent concentrations to optically label the antiCD45 test partitiondistinctly from the IgG test partitions (i.e., the trace is similar tothat in FIG. 21C). In FIG. 22A, the appearance of a signal at about 125ms with no “shoulders” (i.e., lacking the trace that corresponds to FIG.21B as discussed above) indicates a fluid partition that includes noFITC-labeled target. This indicates an unmerged cell droplet, i.e., adroplet that passed through merger 207 without receiving reactionreagents.

The signal at about 725 ms indicates an antiCD45-FITC positive dropletwhile the signal at about 1050 ms indicates an IgG-FITC positive droplet(the tenth and fourteenth droplets to pass the detector, respectively).Here, the tenth and fourteenth droplets are distinguished based on theconcentration of the optical labeling dye (corresponding to the traceshown in FIG. 21C).

FIG. 22B gives a scatter-plot of results relating the traces shown inFIG. 22A. Along the x-axis is plotted an intensity of the antibody labeland the y-axis corresponds to an intensity of a live cell stain.Population 305 corresponds to a CD45 positive population of fluidpartitions and population 301 corresponds to an IgG positive populationof fluid partitions. As unmerged droplets are also counted (e.g., secondsignal in FIG. 22A), the total number of droplets that is prepared canbe accounted for. FIG. 22C shows a histogram corresponding to the plotshown in FIG. 22B. The x-axis is the unitless Bin and the y-axis isfrequency. Such histograms are known in the art for display of flowcytometry results.

FIGS. 23A-23C show ways of controlling or adjusting the dynamic range ofa localized fluorescence assay. As shown in FIG. 23A, an amount offluorescently labeled antibody 215 can be provided in a determinedrelationship to a known or expected number of cell surface markers oncell 219. By controlling the concentration of antibody added (e.g.,through a series of calibration runs), a desired signal of boundantibody can be established that is greater than the dispersedbackground signal.

FIG. 23B shows a method for lowering a strength of a background signal(shown to scale with the diagram shown in FIG. 23A). By making the fluidpartitions larger, fluorescent antibody 215 will be more dispersed whenin the unbound mode. However, when bound on cell 219, the bound signalwill be substantially the same as between FIGS. 23A and 23B. Thus, bycontrolling a volume of a fluid partition, the signal gain can bemodulated and the dynamic range of the assay adjusted.

FIG. 23C shows another way of adjusting the dynamic range by attenuatingthe background signal. Here, partitions included fluorescent antibody215 are merged with partitions (only one is shown) that each contain atleast one cell 219 (which may or may not be expressing the cell surfacemarker, i.e., positive and negative reaction partitions, where onlypositive is shown). A buffer is added to the fluid partitions. Forexample, droplets containing buffer are merged with assay dropletsaccording to methods described herein. The buffer effectively dilutesthe background signal. In certain embodiments, addition of the bufferdoes not substantially change the localized fluorescence signal (e.g.,associated with reaction-positive instances of cell 219). The approachillustrated in FIG. 23C allows for a binding or incubation step toproceed at a substantially higher concentration (e.g., corresponding toconcentration illustrated by left panel of FIG. 23A), while thedetection step can employ a background (non-localized) fluorescence at adifferent concentration.

Localized fluorescence is applicable in combination with other assaysand methods described herein including, for example, bead-capture basedassays that involve rupturing or opening a partition to release thecontents (as the signal may remain localized on the captured bead whenit is, for example, but back into a fluid partition.

Digital Distribution Assays

In some aspects, the invention provides systems and methods fordetecting distributions of molecules. For example, methods of theinvention are useful to detect amounts of gene expression and proteins.In particular, methods of the invention are useful to detect proteinaggregation or complexes. In one example, methods of the invention areused to detect anomalous or unexpected distributions of protein byconducting a chemical reaction that produces a detectable reportindicative of the presence and amount of the protein (e.g., an ELISA orsimilar assay). The results of these assays are compared to expectedresults or control samples in order to determine whether there is ananomalous distribution or amount of a particular protein.

In certain embodiments, the invention is used to determine anomalousprotein aggregation. In samples from the anomalous subset, peptideaggregation or complexes can be detected by the distribution ofreactions in fluid partitions (e.g., digitally), as compared to thedistribution from the non-anomolous rest of the population. Such aphenomenon may arise where a protein is known or suspected to exhibitalternative splicing, binding, or folding pathways or is in a stablecomplex. For example, one protein may be known to be differentlyprocessed (e.g., cleaved by hydrolysis or proteolysis; modified such asby phosphorylation; cross-linked; etc.) such that a complex or aggregateis formed when individuals have some disease propensity or state.

In Alzheimer's disease, for example, when amyloid precursor protein(APP) undergoes proteolysis, the resulting fragments can formaggregations such as fibrils. It is particularly hypothesized that aprotein called tau becomes hyper-phosphorylated, causing the aggregationthat results in neurofibrillary tangles and neuron disintegration. Thus,Alzheimer's disease may generally be associated with an aggregation ofbeta-amyloid protein. Accumulation of aggregated amyloid fibrils mayinduce apoptosis and may inhibit other critical enzyme functions.

This aggregation among proteins can result in there being an anomalous(e.g., non-Poisson) distribution of those proteins when assayed underdilution conditions which should produce Poisson-like statisticdistributions, and this non-standard distribution can provide the basisfor a digital detection assay.

Thus, digital assays are provided that relate to distributions ofproteins and other cellular components. Assays according to methods ofthe invention involve determining an actual distribution and comparingthat to an expected distribution.

FIG. 26 shows histograms corresponding to three different stages ofprotein aggregation. The histogram labeled “normal” indicates anexpected distribution of proteins that are not aggregating. Thehistogram labeled “early” indicates a detected distribution in whichproteins have started exhibiting aggregation. The histogram labeled“late” indicates a detected distribution of proteins that exhibitextensive aggregation.

Assays for digital distribution assays include any assay that canindicate a number of protein molecules per fluid partition. For example,where a protein has one epitope that is available while in eithermonomer or aggregated form, an assay can include antibodies bound tothat epitope(s) coupled to reporters in each fluid partition. Eachantibody can be linked (covalently or non, e.g., through biotin) to anenzyme. Each fluid partition is provided with fluorescently labeledsubstrate for the enzyme that fluoresces when the enzyme catalyzes areaction on the substrate.

A sample is taken from a subject (e.g., a blood sample from a patient).Any desired concentration, isolation, or preparation steps are performedsuch that the target molecules become associated with a reporter fordigital detection in partitions. The sample including the protein ofinterest and reporter is partitioned into fluid partition (thisillustrative example is discussed in terms of a protein, but it will beappreciated that methods of the invention can detect a distribution ofany target thus indicating aggregation or a complex).

Where the fluorescent reporter is the same for all antibodies, thenumber of proteins in each fluid is indicated by the fluorescentintensity of the signal. This can be run in “kinetic” mode, or “endpoint” mode. In end-point mode, each reaction is allowed to run tosubstantially completion, at which point the amount of product hassubstantially plateaued. The amount of product is then detected in eachfluid partition and the number of proteins in each partition iscorrelated to the strength of the signal. The same correlation appliesin kinetic mode. However, measurements are made at one or more timepoints before the amount of product plateaus. Where a whole series oftime points is collect, that time series also gives information aboutenzyme kinetics.

In certain embodiments, where an assay is to be run in kinetic mode, atime point for measurement is first established in an independentcalibration run. A series of droplets are made and incubated. Thedroplets are provided with a dilution of a protein that is known toaggregate and a reporter system (e.g., an enzyme-linked antibody thatbinds to an epitope of the protein). Fluorescence intensity is measuredat multiple time points. For example, where measurement is on-chip andincubation is-off chip, all steps are performed at a temperature atwhich the enzyme exhibits no activity but incubation, which involves atemperature at which the enzyme exhibits activity. For example, R-galexhibits no activity at 4° C., and is active at 37° C. For any givenN-mer of aggregated protein, the fluid partitions that include one suchN-mer will exhibit a characteristic sigmoidal time curve after a seriesof measurements of fluorescence are taken. To discriminate among someset of N-mers, a point along the time trace graph at which thecorresponding sigmoidal time curves exhibit distinct heights is take forthe measurement time.

In some embodiments, an expected distribution (i.e., from a healthyindividual) is known, and an assay need only discriminate between adetected distribution and an expected distribution. Thus where, forexample, an expected distribution has a known ratio of partitions thatinclude 1 target to partitions that include more than one target, anassay can include detecting a ratio of partitions that include 1 targetto partitions that include more than one target that is statisticallysignificantly different than the known ratio. In some embodiments, anon-aggregating particle is expected to exhibit a Poisson ornear-Poisson distribution, and an assay include detecting a number ofdroplets that contain greater than one target molecule, wherein thedetected number does not agree with Poisson or near-Poissondistribution. In some embodiments, a Poisson distribution at a certaindilution is expected to yield a vanishingly small number of fluidpartitions that include two target molecules and zero fluid partitionsthat include greater than two. Thus, an assay can detect a statisticallysignificant number of partitions that includes more than one molecule toindicate the presence of protein aggregation and thus indicate thepresence of a physiological condition. For reference, FIG. 10A shows ameasurement result that may indicate protein aggregation (i.e., notmatch the expected distribution or Poisson).

In an alternative embodiment, each fluid partition is provided withenzyme linked antibodies in which all of the antibodies are the same,but a fraction (e.g., half) is linked to one enzyme that operates on onesubstrate to generate one reporter, and another portion of theantibodies are linked to another enzyme that catalyzes a reaction thatproduces a different reporter. In this example, assuming one reporter isblue and one is yellow, some number of fluid partitions that have morethan one protein will produce both the blue and the yellow reporter. Ifthe protein is not aggregating, at a certain dilution, it can beexpected that blue and yellow will be found together in only some numberof droplets (e.g., zero, or 0.00001% of them). In this example,detecting a blue with yellow in a greater number of droplets (e.g.,0.05%, 1%, etc.) indicates the protein is aggregating.

In distribution assays in which signal strength indicates a number ofproteins in the droplet, for a given dilution of sample into droplets,assuming random distribution of a non-aggregating protein, there will bea characteristic expected distribution. Even for a protein that exhibitssome aggregation in normal conditions, there will be a characteristicexpected distribution. In certain embodiments, the expected distributionis predicted by Poisson or is Poisson-like. A substantially large numberof droplets will contain zero proteins. A substantially majority of thedroplets that contain any protein will contain 1 protein. Some small(maybe vanishingly small) number of protein-containing droplets willcontain 2 or more.

In the case where the proteins aggregate, such an expected distributionwill not obtain. For example, for a fully aggregated protein (e.g.,“late” stage) that aggregates into 4-mers, a substantially large numberof droplets will contain zero proteins and a substantial majority of thedroplets that contain any protein will contain four proteins, as isillustrated in FIG. 26.

Furthermore, aggregation can be detected over time. That is, earlystages of aggregation will exhibit an non-expected distribution. In someembodiments, protein folding into tertiary structures and/or quaternaryassembly is studied over the course of, for example, minutes, hours, ordays. In certain embodiments, a distribution of aggregation in a sampleindicates a stage of progression of an aggregation-related conditionthat takes months, years, or decades to progress. For example, latestage distributions may only be expected after about 50 or 75 years.However, an assay run at an earlier time period (e.g., 15 or 25 years)may indicate an “early” stage aggregation distribution, as shown in FIG.26.

In certain aspects, the invention provides a method for detecting aphysiological condition in a human that includes forming fluidpartitions that include components of a chemical reaction, in which atleast one of the components has a detectable label that is acted on bythe chemical reaction. The reaction proceeds in the partitions, and anumber of reaction-positive partitions is identified and an amount ofthe component is determined. A statistically expected distribution oramount of the component is computed and compared to the actualdistribution or amount. The results of the comparison can indicate thepresence of an aggregation phenomenon.

In some embodiments, the invention provides a method for testing aresponse to a treatment for a condition or for monitoring a progressionof a condition. A condition includes conditions that characterized byaggregation such as, for example, Alzheimer's disease. Determining aresponse to treatment is included in methods for development oftreatments such as, for example, drug development. In some aspects, acandidate drug is tested (e.g., administered). A sample is taken and adistribution of molecules is determined. The molecules can be a proteinsuch as beta-amyloid. Based on the determined distribution, aneffectiveness of the drug is evaluated and a recommendation can be made.In some aspects, progress of a disease is monitored by methods thatinclude taking a sample and determining a distribution of moleculeswithin the sample according to methodologies described herein.

Digital distribution assays of the invention are highly sensitive andcan proceed quickly with very small samples. For example, a 5 mLbiological sample can be assayed in less than a day (e.g., about anhour), and a stage of aggregation can be determined.

In certain embodiments, the protein is beta-amyloid. A sample of humanblood can be taken for the assay. An expected distribution can becalculated (e.g., statistically according to Poisson), derivedempirically (e.g., sampling numerous members of a population for themajority pattern), or obtained from a reference such as a digital fileor chart. Accordingly, in some embodiments, the invention offers a bloodtest for Alzheimer's disease. In certain embodiments, an assay of theinvention can be performed on a patient at any life stage (e.g.,childhood, teens, etc.). It will be appreciated that any aggregationpattern may be subject to detection by a digital distribution assay andaggregation generally includes the reverse phenomenon of fragmentation.As such, targets for a digital distribution assay may include peptides,nucleic acids, carbohydrates, lipids, or other molecules. A distributionassay can determine a stage of fragmentation as well as a stage ofpolymerization (e.g., esterification, poly peptide formation,carbohydrate cross-linking, synthetic polymerization, etc.).

Droplet Formation

Methods of the invention involve forming sample droplets. The dropletsare aqueous droplets that are surrounded by an immiscible carrier fluid.Methods of forming such droplets are shown for example in Link et al.(U.S. patent application numbers 2008/0014589, 2008/0003142, and2010/0137163), Stone et al. (U.S. Pat. No. 7,708,949 and U.S. patentapplication number 2010/0172803), Anderson et al. (U.S. Pat. No.7,041,481 and which reissued as RE41,780) and European publicationnumber EP2047910 to RainDance Technologies Inc. The content of each ofwhich is incorporated by reference herein in its entirety. Droplets canbe formed with various uniform sizes, a non-uniform size, or a range ofsizes.

FIG. 24 shows an exemplary embodiment of a device 100 for dropletformation. Device 100 includes an inlet channel 101, and outlet channel102, and two carrier fluid channels 103 and 104. Channels 101,102,103,and 104 meet at a junction 105. Inlet channel 101 flows sample fluid tothe junction 105. Carrier fluid channels 103 and 104 flow a carrierfluid that is immiscible with the sample fluid to the junction 105.Inlet channel 101 narrows at its distal portion wherein it connects tojunction 105 (See FIG. 25). Inlet channel 101 is oriented to beperpendicular to carrier fluid channels 103 and 104. Droplets are formedas sample fluid flows from inlet channel 101 to junction 105, where thesample fluid interacts with flowing carrier fluid provided to thejunction 105 by carrier fluid channels 103 and 104. Outlet channel 102receives the droplets of sample fluid surrounded by carrier fluid.

The sample fluid is typically an aqueous buffer solution, such asultrapure water (e.g., 18 mega-ohm resistivity, obtained, for example bycolumn chromatography), 10 mM Tris HCl and 1 mM EDTA (TE) buffer,phosphate buffer saline (PBS) or acetate buffer. Any liquid or bufferthat is physiologically compatible with enzymes can be used. The carrierfluid is immiscible with the sample fluid. The carrier fluid can be anon-polar solvent, decane (e g., tetradecane or hexadecane),fluorocarbon oil, silicone oil or another oil (for example, mineraloil).

In certain embodiments, the carrier fluid contains one or moreadditives, such as agents which reduce surface tensions (surfactants).Surfactants can include Tween, Span, fluorosurfactants, and other agentsthat are soluble in oil relative to water. In some applications,performance is improved by adding a second surfactant. Surfactants canaid in controlling or optimizing droplet size, flow and uniformity, forexample by reducing the shear force needed to extrude or inject dropletsinto a channel. This can affect droplet volume and periodicity, or therate or frequency at which droplets break off into an intersectingchannel. Furthermore, the surfactant can serve to stabilize aqueousemulsions in fluorinated oils from coalescing.

In certain embodiments, the droplets may be coated with a surfactant.Preferred surfactants that may be added to the carrier fluid include,but are not limited to, surfactants such as sorbitan-based carboxylicacid esters (e.g., the “Span” surfactants, Fluka Chemika), includingsorbitan monolaurate (Span 20), sorbitan monopalmitate (Span 40),sorbitan monostearate (Span 60) and sorbitan monooleate (Span 80), andperfluorinated polyethers (e.g., DuPont Krytox 157 FSL, FSM, and/orFSH). Other non-limiting examples of non-ionic surfactants which may beused include polyoxyethylenated alkylphenols (for example, nonyl-,P-dodecyl-, and dinonylphenols), polyoxyethylenated straight chainalcohols, polyoxyethylenated polyoxypropylene glycols,polyoxyethylenated mercaptans, long chain carboxylic acid esters (forexample, glyceryl and polyglyceryl esters of natural fatty acids,propylene glycol, sorbitol, polyoxyethylenated sorbitol esters,polyoxyethylene glycol esters, etc.) and alkanolamines (e.g.,diethanolamine-fatty acid condensates and isopropanolamine-fatty acidcondensates).

In certain embodiments, the carrier fluid may be caused to flow throughthe outlet channel so that the surfactant in the carrier fluid coats thechannel walls. In one embodiment, the fluorosurfactant can be preparedby reacting the perflourinated polyether DuPont Krytox 157 FSL, FSM, orFSH with aqueous ammonium hydroxide in a volatile fluorinated solvent.The solvent and residual water and ammonia can be removed with a rotaryevaporator. The surfactant can then be dissolved (e.g., 2.5 wt. %) in afluorinated oil (e.g., Fluorinert (3M)), which then serves as thecarrier fluid.

Unknown or known analytes or compounds over a very wide dynamic range ofconcentrations can be merged with droplets containing single or multipleenzyme molecules and reporters via the use of a Taylor dispersion thatforms upstream of the droplet forming nozzle. Co-encapsulation of anoptical dye that has similarly been dispersed via a Taylor flow profilecan be used to track the analyte/compound concentration. (see, e.g.,Miller, et al., PNAS 109(2):378-383 (2012); U.S. Pat. No. 7,039,527; andU.S. Pub. 2011/0063943, the contents of which are hereby incorporated byreference in their entirety).

In certain embodiments, an aliquot of a sample is aspirated into a PEEKtubing, such that a slug of the sample is in the PEEK tubing with asubstantially uniform concentration. The tubing is inserted into a portinto a microfluidic channel, and the sample enters the channel forming aconcentration gradient in the aqueous phase, the gradient generallyfollowing Taylor-Aris dispersion mechanics. The sample fluid joins thecarrier fluid first having a vanishingly small concentration and thenincreasing up a gradient asymptotically until a maximum (e.g., 10micromolar) is reached, after which it decreases similarly. The fluid isflowed to a droplet nozzle, where a series of droplets are made. Thesample can be pushed into the channel via a pump, a plunger, or bedriven by pressure (e.g., from a gas tank).

In certain embodiments, the dispersion is created for each partition ofa plurality (e.g., for numerous or all wells from a 96 well plate, inwhich every well has a target sample such as a small molecule). Systemsand methods of the invention provide a series of microdroplets in whichthe contents have a controlled concentration gradient through a simpleinjection procedure. Further, the sample can be spiked with a dye havinga known concentration, and the dye concentration can be measureddownstream (e.g., during or after any other assay). The measured dyeconcentrations can be used to determine the sample concentration.

By methods and systems provided here, a controlled gradient ofconcentrations of one or more sample aliquots can be merged withdroplets that include a single target such as a single enzyme molecule.Enzyme activity can be assayed and kinetics studied. For example,individual enzyme molecules can be tested against a concentration rangeof activators, inhibitors, etc.

Substrates or other reaction or reporter components may beco-encapsulated into droplets with the enzyme without mixing beforedroplet formation by ‘co-flow’ of the separate components. When co-flowis used, each separate component is flowed to the microfluidic channelupstream of the droplet-forming nozzle, and both components flow in alaminar fashion to the nozzle without mixing. In co-flow methods,components are flowed in parallel streams through a channel. Due to flowdynamics, the contents of the streams do not mix until they hit thelambda injector or droplet forming nozzle. Two separate streams can beco-flowed, or three, four, or more. Where hardware is configured for Nstreams, and N−1 streams containing reaction components are desired, a“dummy” stream of water or saline can be included.

Another technique for forming droplets including enzymes and substratesfrom different fluids or previously generated droplets involves dropletmerging. The merging of droplets can be accomplished using, for example,one or more droplet merging techniques described for example in Link etal. (U.S. patent application numbers 2008/0014589, 2008/0003142, and2010/0137163) and European publication number EP2047910 to RaindanceTechnologies Inc. In embodiments involving merging of droplets, twodroplet formation modules are used. A first droplet formation moduleproduces the droplets including enzymes. A second droplet formationmodule produces droplets that contain substrate. The droplet formationmodules are arranged and controlled to produce an interdigitation ofdroplets flowing through a channel. Such an arrangement is described forexample in Link et al. (U.S. patent application numbers 2008/0014589,2008/0003142, and 2010/0137163) and European publication numberEP2047910 to Raindance Technologies Inc.

Droplets are then caused to merge, producing a droplet that includesenzymes and substrates. Droplets may be merged for example by: producingdielectrophoretic forces on the droplets using electric field gradientsand then controlling the forces to cause the droplets to merge;producing droplets of different sizes that thus travel at differentvelocities, which causes the droplets to merge; and producing dropletshaving different viscosities that thus travel at different velocities,which causes the droplets to merge with each other. Each of thosetechniques is further described in Link et al. (U.S. patent applicationnumbers 2008/0014589, 2008/0003142, and 2010/0137163) and Europeanpublication number EP2047910 to Raindance Technologies Inc. Furtherdescription of producing and controlling dielectrophoretic forces ondroplets to cause the droplets to merge is described in Link et al.(U.S. patent application number 2007/0003442) and European Patent NumberEP2004316 to Raindance Technologies Inc. Additional methods may be usedfor controlled droplet merging, for example by altering the flowprofiles of paired droplets via properly constrained microfluidicchannel design. Merges can be performed in a successive fashion,enabling step-wise addition of substrates, reagents, or reaction stepcomponents.

Another approach to forming a droplet including enzymes and substratesinvolves forming a droplet including enzymes, and contacting the dropletwith a fluid stream including substrate, in which a portion of the fluidstream integrates with the droplet to form a droplet including enzymesand substrates. In this approach, only one phase needs to reach a mergearea in a form of a droplet. Further description of such method is shownin the co-owned and co-pending U.S. patent applications to Yurkovetsky,(U.S. patent application Ser. No. 61/441,985 and U.S. patent applicationSer. No. 13/371,222), the content of which is incorporated by referenceherein in its entirety.

A droplet is formed as described above. After formation of the dropletis contacted with a flow of a second sample fluid stream. Contactbetween the droplet and the fluid stream results in a portion of thefluid stream integrating with the droplet to form a droplet includingnucleic acid from different samples.

The monodisperse droplets of the first sample fluid flow through a firstchannel separated from each other by immiscible carrier fluid andsuspended in the immiscible carrier fluid. The droplets are delivered tothe merge area, i.e., junction of the first channel with the secondchannel, by a pressure-driven flow generated by a positive displacementpump. While droplet arrives at the merge area, a bolus of a secondsample fluid is protruding from an opening of the second channel intothe first channel. Preferably, the channels are oriented perpendicularto each other. However, any angle that results in an intersection of thechannels may be used.

The bolus of the second sample fluid stream continues to increase insize due to pumping action of a positive displacement pump connected tochannel, which outputs a steady stream of the second sample fluid intothe merge area. The flowing droplet containing the first sample fluideventually contacts the bolus of the second sample fluid that isprotruding into the first channel. Contact between the two sample fluidsresults in a portion of the second sample fluid being segmented from thesecond sample fluid stream and joining with the first sample fluiddroplet to form a mixed droplet. In certain embodiments, each incomingdroplet of first sample fluid is merged with the same amount of secondsample fluid.

In certain embodiments, an electric charge is applied to the first andsecond sample fluids. Description of applying electric charge to samplefluids is provided in Link et al. (U.S. patent application number2007/0003442) and European Patent Number EP2004316 to RaindanceTechnologies Inc. (Lexington, Mass.), the content of each of which isincorporated by reference herein in its entirety. Electric charge may becreated in the first and second sample fluids within the carrier fluidusing any suitable technique, for example, by placing the first andsecond sample fluids within an electric field (which may be AC, DC,etc.), and/or causing a reaction to occur that causes the first andsecond sample fluids to have an electric charge, for example, a chemicalreaction, an ionic reaction, a photocatalyzed reaction, etc.

The electric field, in some embodiments, is generated from an electricfield generator, i.e., a device or system able to create an electricfield that can be applied to the fluid. The electric field generator mayproduce an AC field (i.e., one that varies periodically with respect totime, for example, sinusoidally, sawtooth, square, etc.), a DC field(i.e., one that is constant with respect to time), a pulsed field, etc.The electric field generator may be constructed and arranged to createan electric field within a fluid contained within a channel or amicrofluidic channel. The electric field generator may be integral to orseparate from the fluidic system containing the channel or microfluidicchannel, according to some embodiments.

Techniques for producing a suitable electric field (which may be AC, DC,etc.) are known to those of ordinary skill in the art. For example, inone embodiment, an electric field is produced by applying voltage acrossa pair of electrodes, which may be positioned on or embedded within thefluidic system (for example, within a substrate defining the channel ormicrofluidic channel), and/or positioned proximate the fluid such thatat least a portion of the electric field interacts with the fluid. Theelectrodes can be fashioned from any suitable electrode material ormaterials known to those of ordinary skill in the art, including, butnot limited to, silver, gold, copper, carbon, platinum, copper,tungsten, tin, cadmium, nickel, indium tin oxide (“ITO”), etc., as wellas combinations thereof. In some cases, transparent or substantiallytransparent electrodes can be used.

The electric field facilitates rupture of the interface separating thesecond sample fluid and the droplet. Rupturing the interface facilitatesmerging of bolus of the second sample fluid and the first sample fluiddroplet. The forming mixed droplet continues to increase in size untilit a portion of the second sample fluid breaks free or segments from thesecond sample fluid stream prior to arrival and merging of the nextdroplet containing the first sample fluid. The segmenting of the portionof the second sample fluid from the second sample fluid stream occurs assoon as the shear force exerted on the forming mixed droplet by theimmiscible carrier fluid overcomes the surface tension whose action isto keep the segmenting portion of the second sample fluid connected withthe second sample fluid stream. The now fully formed mixed dropletcontinues to flow through the first channel.

Droplet Sorting

Methods of the invention may further include sorting the droplets. Asorting module may be a junction of a channel where the flow of dropletscan change direction to enter one or more other channels, e.g., a branchchannel, depending on a signal received in connection with a dropletinterrogation in the detection module. Typically, a sorting module ismonitored and/or under the control of the detection module, andtherefore a sorting module may correspond to the detection module. Thesorting region is in communication with and is influenced by one or moresorting apparatuses.

A sorting apparatus includes techniques or control systems, e.g.,dielectric, electric, electro-osmotic, (micro-) valve, etc. A controlsystem can employ a variety of sorting techniques to change or directthe flow of molecules, cells, small molecules or particles into apredetermined branch channel. A branch channel is a channel that is incommunication with a sorting region and a main channel. The main channelcan communicate with two or more branch channels at the sorting moduleor branch point, forming, for example, a T-shape or a Y-shape. Othershapes and channel geometries may be used as desired. Typically, abranch channel receives droplets of interest as detected by thedetection module and sorted at the sorting module. A branch channel canhave an outlet module and/or terminate with a well or reservoir to allowcollection or disposal (collection module or waste module, respectively)of the molecules, cells, small molecules or particles. Alternatively, abranch channel may be in communication with other channels to permitadditional sorting.

A characteristic of a fluidic droplet may be sensed and/or determined insome fashion, for example, as described herein (e.g., fluorescence ofthe fluidic droplet may be determined), and, in response, an electricfield may be applied or removed from the fluidic droplet to direct thefluidic droplet to a particular region (e.g. a channel). In certainembodiments, a fluidic droplet is sorted or steered by inducing a dipolein the uncharged fluidic droplet (which may be initially charged oruncharged), and sorting or steering the droplet using an appliedelectric field. The electric field may be an AC field, a DC field, etc.For example, a channel containing fluidic droplets and carrier fluid,divides into first and second channels at a branch point. Generally, thefluidic droplet is uncharged. After the branch point, a first electrodeis positioned near the first channel, and a second electrode ispositioned near the second channel. A third electrode is positioned nearthe branch point of the first and second channels. A dipole is theninduced in the fluidic droplet using a combination of the electrodes.The combination of electrodes used determines which channel will receivethe flowing droplet. Thus, by applying the proper electric field, thedroplets can be directed to either the first or second channel asdesired. Further description of droplet sorting is shown for example inLink et al. (U.S. patent application numbers 2008/0014589, 2008/0003142,and 2010/0137163) and European publication number EP2047910 to RaindanceTechnologies Inc.

Droplet sorting relates to methods and systems described herein byallowing one to detect the effect of an enzymatic reaction in a fluidpartition (or absence thereof) and to selectively examine that specificpartition further. For example, where a specific class of molecule isbeing assayed for, an enzyme-positive droplet can be sorted andseparated from the rest. That specific droplet can be “broken open” andits contents further examined. For example, a cDNA library can beprepared from all RNA (e.g., mRNA) in that droplet. Nucleic acids canthen be sequenced.

Release from Droplets

Methods of the invention may further involve releasing the enzymes orproducts or other identifiable material from the droplets for furtheranalysis. Methods of releasing contents from the droplets are shown forexample in Link et al. (U.S. patent application numbers 2008/0014589,2008/0003142, and 2010/0137163) and European publication numberEP2047910 to Raindance Technologies Inc.

In certain embodiments, sample droplets are allowed to cream to the topof the carrier fluid. By way of non-limiting example, the carrier fluidcan include a perfluorocarbon oil that can have one or more stabilizingsurfactants. The droplet rises to the top or separates from the carrierfluid by virtue of the density of the carrier fluid being greater thanthat of the aqueous phase that makes up the droplet. For example, theperfluorocarbon oil used in one embodiment of the methods of theinvention is 1.8, compared to the density of the aqueous phase of thedroplet, which is 1.0.

The creamed liquids are then placed onto a second carrier fluid whichcontains a de-stabilizing surfactant, such as a perfluorinated alcohol(e.g. 1H,1H,2H,2H-Perfluoro-1-octanol). The second carrier fluid canalso be a perfluorocarbon oil. Upon mixing, the aqueous droplets beginsto coalesce, and coalescence is completed by brief centrifugation at lowspeed (e.g., 1 minute at 2000 rpm in a microcentrifuge). The coalescedaqueous phase can now be removed and further analyzed.

Definitions

The terms used in this specification generally have their ordinarymeanings in the art, within the context of this invention and in thespecific context where each term is used. Certain terms are discussedbelow, or elsewhere in the specification, to provide additional guidanceto the practitioner in describing the devices and methods of theinvention and how to make and use them. It will be appreciated that thesame thing can typically be described in more than one way.Consequently, alternative language and synonyms may be used for any oneor more of the terms discussed herein. Synonyms for certain terms areprovided. However, a recital of one or more synonyms does not excludethe use of other synonyms, nor is any special significance to be placedupon whether or not a term is elaborated or discussed herein. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference. In the case of conflict,the present specification, including definitions, will control. Inaddition, the materials, methods, and examples are illustrative only andare not intended to be limiting.

The invention is also described by means of particular examples.However, the use of such examples anywhere in the specification,including examples of any terms discussed herein, is illustrative onlyand in no way limits the scope and meaning of the invention or of anyexemplified term. Likewise, the invention is not limited to anyparticular preferred embodiments described herein. Indeed, manymodifications and variations of the invention will be apparent to thoseskilled in the art upon reading this specification and can be madewithout departing from its spirit and scope. The invention is thereforeto be limited only by the terms of the appended claims along with thefull scope of equivalents to which the claims are entitled.

As used herein, “about” or “approximately” shall generally mean within20 percent, preferably within 10 percent, and more preferably within 5percent of a given value or range.

The term “molecule” means any distinct or distinguishable structuralunit of matter comprising one or more atoms, and includes for examplepolypeptides and polynucleotides.

The term “polymer” means any substance or compound that is composed oftwo or more building blocks (‘mers’) that are repetitively linked toeach other. For example, a “dimer” is a compound in which two buildingblocks have been joined together.

The term “polynucleotide” as used herein refers to a polymeric moleculehaving a backbone that supports bases capable of hydrogen bonding totypical polynucleotides, where the polymer backbone presents the basesin a manner to permit such hydrogen bonding in a sequence specificfashion between the polymeric molecule and a typical polynucleotide(e.g., single-stranded DNA). Such bases are typically inosine,adenosine, guanosine, cytosine, uracil and thymidine. Polymericmolecules include double and single stranded RNA and DNA, and backbonemodifications thereof, for example, methylphosphonate linkages.

Thus, a “polynucleotide” or “nucleotide sequence” is a series ofnucleotide bases (also called “nucleotides”) generally in DNA and RNA,and means any chain of two or more nucleotides. A nucleotide sequencetypically carries genetic information, including the information used bycellular machinery to make proteins and enzymes. These terms includedouble or single stranded genomic and cDNA, RNA, any synthetic andgenetically manipulated polynucleotide, and both sense and anti-sensepolynucleotide (although only sense stands are being representedherein).

This includes single- and double-stranded molecules, i.e., DNA-DNA,DNA-RNA and RNA-RNA hybrids, as well as “protein nucleic acids” (PNA)formed by conjugating bases to an amino acid backbone. This alsoincludes nucleic acids containing modified bases, for examplethio-uracil, thio-guanine and fluoro-uracil.

The polynucleotides herein may be flanked by natural regulatorysequences, or may be associated with heterologous sequences, includingpromoters, enhancers, response elements, signal sequences,polyadenylation sequences, introns, 5′- and 3′-non-coding regions, andthe like. The nucleic acids may also be modified by many means known inthe art. Non-limiting examples of such modifications includemethylation, “caps”, substitution of one or more of the naturallyoccurring nucleotides with an analog, and internucleotide modificationssuch as, for example, those with uncharged linkages (e.g., methylphosphonates, phosphotriesters, phosphoroamidates, carbamates, etc.) andwith charged linkages (e.g., phosphorothioates, phosphorodithioates,etc.). Polynucleotides may contain one or more additional covalentlylinked moieties, such as, for example, proteins (e.g., nucleases,toxins, antibodies, signal peptides, poly-L-lysine, etc.), intercalators(e.g., acridine, psoralen, etc.), chelators (e.g., metals, radioactivemetals, iron, oxidative metals, etc.), and alkylators. Thepolynucleotides may be derivatized by formation of a methyl or ethylphosphotriester or an alkyl phosphoramidate linkage. Furthermore, thepolynucleotides herein may also be modified with a label capable ofproviding a detectable signal, either directly or indirectly. Exemplarylabels include radioisotopes, fluorescent molecules, biotin, and thelike.

The term “dielectrophoretic force gradient” means a dielectrophoreticforce is exerted on an object in an electric field provided that theobject has a different dielectric constant than the surrounding media.This force can either pull the object into the region of larger field orpush it out of the region of larger field. The force is attractive orrepulsive depending respectively on whether the object or thesurrounding media has the larger dielectric constant.

“DNA” (deoxyribonucleic acid) means any chain or sequence of thechemical building blocks adenine (A), guanine (G), cytosine (C) andthymine (T), called nucleotide bases, that are linked together on adeoxyribose sugar backbone. DNA can have one strand of nucleotide bases,or two complimentary strands which may form a double helix structure.“RNA” (ribonucleic acid) means any chain or sequence of the chemicalbuilding blocks adenine (A), guanine (G), cytosine (C) and uracil (U),called nucleotide bases, that are linked together on a ribose sugarbackbone. RNA typically has one strand of nucleotide bases.

A “polypeptide” (one or more peptides) is a chain of chemical buildingblocks called amino acids that are linked together by chemical bondscalled peptide bonds. A “protein” is a polypeptide produced by a livingorganism. A protein or polypeptide may be “native” or “wild-type”,meaning that it occurs in nature; or it may be a “mutant”, “variant” or“modified”, meaning that it has been made, altered, derived, or is insome way different or changed from a native protein, or from anothermutant.

An “enzyme” is a polypeptide molecule, usually a protein produced by aliving organism, that catalyzes chemical reactions of other substances.The enzyme is not itself altered or destroyed upon completion of thereaction, and can therefore be used repeatedly to catalyze reactions. A“substrate” refers to any substance upon which an enzyme acts.

As used herein, “particles” means any substance that may be encapsulatedwithin a droplet for analysis, reaction, sorting, or any operationaccording to the invention. Particles are not only objects such asmicroscopic beads (e.g., chromatographic and fluorescent beads), latex,glass, silica or paramagnetic beads, but also includes otherencapsulating porous and/or biomaterials such as liposomes, vesicles andother emulsions. Beads ranging in size from 0.1 micron to 1 mm can beused in the devices and methods of the invention and are thereforeencompassed with the term “particle” as used herein. The term particlealso encompasses biological cells, as well as beads and othermicroscopic objects of similar size (e.g., from about 0.1 to 120microns, and typically from about 1 to 50 microns) or smaller (e.g.,from about 0.1 to 150 nm). The devices and methods of the invention arealso directed to sorting and/or analyzing molecules of any kind,including polynucleotides, polypeptides and proteins (including enzymes)and their substrates and small molecules (organic or inorganic). Thus,the term particle further encompasses these materials.

The particles (including, e.g., cells and molecules) are sorted and/oranalyzed by encapsulating the particles into individual droplets (e.g.,droplets of aqueous solution in oil), and these droplets are thensorted, combined and/or analyzed in a microfabricated device.Accordingly, the term “droplet” generally includes anything that is orcan be contained within a droplet.

A “small molecule” or “small molecule chemical compound” as used herein,is meant to refer to a composition that has a molecular weight of lessthan 500 Daltons. Small molecules are distinguished frompolynucleotides, polypeptides, carbohydrates and lipids.

As used herein, “cell” means any cell or cells, as well as viruses orany other particles having a microscopic size, e.g. a size that issimilar to or smaller than that of a biological cell, and includes anyprokaryotic or eukaryotic cell, e.g., bacteria, fungi, plant and animalcells. Cells are typically spherical, but can also be elongated,flattened, deformable and asymmetrical, i.e., non-spherical. The size ordiameter of a cell typically ranges from about 0.1 to 120 microns, andtypically is from about 1 to 50 microns. A cell may be living or dead.Since the microfabricated device of the invention is directed to sortingmaterials having a size similar to a biological cell (e.g. about 0.1 to120 microns) or smaller (e.g., about 0.1 to 150 nm) any material havinga size similar to or smaller than a biological cell can be characterizedand sorted using the microfabricated device of the invention. Thus, theterm cell shall further include microscopic beads (such aschromatographic and fluorescent beads), liposomes, emulsions, or anyother encapsulating biomaterials and porous materials. Non-limitingexamples include latex, glass, orparamagnetic beads; and vesicles suchas emulsions and liposomes, and other porous materials such as silicabeads. Beads ranging in size from 0.1 micron to 1 mm can also be used,for example in sorting a library of compounds produced by combinatorialchemistry. As used herein, a cell may be charged or uncharged. Forexample, charged beads may be used to facilitate flow or detection, oras a reporter. Biological cells, living or dead, may be charged forexample by using a surfactant, such as SDS (sodium dodecyl sulfate). Theterm cell further encompasses “virions”, whether or not virions areexpressly mentioned.

A “virion”, “virus particle” is the complete particle of a virus.Viruses typically comprise a nucleic acid core (comprising DNA or RNA)and, in certain viruses, a protein coat or “capsid”. Certain viruses mayhave an outer protein covering called an “envelope”. A virion may beeither living (i.e., “viable”) or dead (i.e., “non-viable”). A living or“viable” virus is one capable of infecting a living cell. Viruses aregenerally smaller than biological cells and typically range in size fromabout 20-25 nm diameter or less (parvoviridae, picomoviridae) toapproximately 200-450 nm (poxviridae). However, some filamentous virusesmay reach lengths of 2000 nm (closterviruses) and are therefore largerthan some bacterial cells. Since the microfabricated device of theinvention is particularly suited for sorting materials having a sizesimilar to a virus (i.e., about 0.1 to 150 nm), any material having asize similar to a virion can be characterized and sorted using themicrofabricated device of the invention. Non-limiting examples includelatex, glass or paramagnetic beads; vesicles such as emulsions andliposomes; and other porous materials such as silica beads. Beadsranging in size from 0.1 to 150 nm can also be used, for example, insorting a library of compounds produced by combinatorial chemistry. Asused herein, a virion may be charged or uncharged. For example, chargedbeads may be used to facilitate flow or detection, or as a reporter.Biological viruses, whether viable or non-viable, may be charged, forexample, by using a surfactant, such as SDS.

A “reporter” is any molecule, or a portion thereof, that is detectable,or measurable, for example, by optical detection. In addition, thereporter associates with a molecule, cell or virion or with a particularmarker or characteristic of the molecule, cell or virion, or is itselfdetectable to permit identification of the molecule, cell or virion's,or the presence or absence of a characteristic of the molecule, cell orvirion. In the case of molecules such as polynucleotides suchcharacteristics include size, molecular weight, the presence or absenceof particular constituents or moieties (such as particular nucleotidesequences or restrictions sites). In the case of cells, characteristicswhich may be marked by a reporter includes antibodies, proteins andsugar moieties, receptors, polynucleotides, and fragments thereof. Theterm “label” can be used interchangeably with “reporter”. The reporteris typically a dye, fluorescent, ultraviolet, or chemiluminescent agent,chromophore, or radio-label, any of which may be detected with orwithout some kind of stimulatory event, e.g., fluoresce with or withouta reagent. In one embodiment, the reporter is a protein that isoptically detectable without a device, e.g. a laser, to stimulate thereporter, such as horseradish peroxidase (HRP). A protein reporter canbe expressed in the cell that is to be detected, and such expression maybe indicative of the presence of the protein or it can indicate thepresence of another protein that may or may not be coexpressed with thereporter. A reporter may also include any substance on or in a cell thatcauses a detectable reaction, for example by acting as a startingmaterial, reactant or a catalyst for a reaction which produces adetectable product. Cells may be sorted, for example, based on thepresence of the substance, or on the ability of the cell to produce thedetectable product when the reporter substance is provided.

A “marker” is a characteristic of a molecule, cell or virion that isdetectable or is made detectable by a reporter, or which may becoexpressed with a reporter. For molecules. a marker can be particularconstituents or moieties, such as restrictions sites or particularnucleic acid sequences in the case of polynucleotides. For cells andvirions, characteristics may include a protein, including enzyme,receptor and ligand proteins, saccharrides, polynucleotides, andcombinations thereof, or any biological material associated with a cellor virion. The product of an enzymatic reaction may also be used as amarker. The marker may be directly or indirectly associated with thereporter or can itself be a reporter. Thus, a marker is generally adistinguishing feature of a molecule, cell or virion, and a reporter isgenerally an agent which directly or indirectly identifies or permitsmeasurement of a marker. These terms may, however, be usedinterchangeably.

The invention is further described below, by way of the followingexamples. The examples also illustrate useful methodology for practicingthe invention. These examples do not limit the claimed invention.

EXAMPLES Example 1

Example 1 shows methods of surfactant syntheses.

Below of the reaction scheme for creating the surfactants utilized instabilizing the droplet libraries provided by the instant invention.

Reagent Table is as follows:

Moles/ Amount Other (density, Name MW Equiv. used purity, safety, misc.)Krytox FSH 6500 1.54 mmol 10.0 g (1 eq) Oxalyl 126.93 15.4 mmol 1.3 mL d= 1.5 g/mL; Chloride (10 eq) (1.95 g) b.p. 62-65° C. HFE 7100 250.06 50mL b.p. 61° C.

The procedure includes, adding 10.0 (1.54 mmol; eq) of Krytox acid FSHin 50 mL HIFE 7100 (not anhydrous) at right under Ar was added 1.95 g(15.4 mmol; 10 eq) of Oxalyl Chloride dropwise. Stirred 10 min, then thereaction was warmed to gentle reflux (note boiling points of solvent andreagent). Some bubbling was noted, even before reaction had reachedreflux. Continued overnight.

The following day, the reaction was very slightly cloudy, and containeda very small amount of a yellow solid. Cooled, HFE and excess Oxalylchloride evaporated. Residue dissolved in 40 mL fresh HFFE, thenfiltered to remove the solid. FE evaporated again, residue placed underhivac for 1 hr. Yield of a cloudy white oil 10.14 g. Used withoutfurther purification.

The reagent table is as follows:

Moles/ Amount Other (density, Name MW Equiv. used purity, safety, misc.)JSJ 73-019 6518 1.55 mmol 10.14 g used crude (2 eq) JSJ 73-006 568 0.77mmol 0.441 g (1 eq) Triethylamine 101.19 2.33 mmol 0.325 mL d = 0.726;b.p. 88° C. (3 eq) Tetrahydrofuran 20 mL b.p. 66° C. FC 3283 521 40 mLb.p. 123-33° C.; dried over CaSO₄

The procedure includes, drying the amine was by placing under hivacrotovap at a bath temp of 60° C. for 4 hrs. To a solution of 0.441 g(0.77 mmol; 1 eq) of PEG 600 diamine J and 0.325 mL (2.33 mmol; 3 eq) ofEt₃N in 20 ml an hydrous THF at rt under Ar was added a solution of10.14 g (1.55 mmol; 2 eq) of crude JSJ 73-019 in 40 mL FC 3283. A whiteprecipitate (Et₃N.HCl) was noted to form in the reaction and on theflask walls. The milky-white two-phase suspension was stirred wellovernight.

The THF and most FC was evaporated. This left a solid residue dispersedin the FC solvent (Et₃N.HCl). Oil residue diluted with 50 mL FC3283,then filtered through Celite. Celite washed with 2×30 mL FC 3283. Thesolid left in the flask was found to be water soluble, suggesting thatit was Et₃N.HCl. The filtrate was cloudy white. FC 3283 evaporated usinghivac and 60° C. bath. Kept as such for ˜1.5 hrs to evaporate allsolvent.

Sample submitted for 19F NMR. Peak for the CF was in the correctposition, indicating amide had formed

The reagent table is as follows:

Moles/ Amount Other (density, Name MW Equiv. used purity, safety, misc.)PEG 600 600 0.125 75.0 g Avg. MW 600; (Fluka) (1 eq) CAS 25322-65-3;m.p. 17-22° C. p-Toluene 190.65 0.283 53.93 g Sulfonyl (2.3 eq) chlorideTetrahydrofuran 525 mL b.p. 66° C., not anhydrous Sodium 40.00 0.50620.25 g Hydroxide (4.05 eq) Water 156 mL

The procedure included adding to a solution of 20.25 g (0.506 mol; 4.05eq) of NaOH in 156 mL water cooled in an ice-bath to ˜0° C. (not underinert atmosphere) was added a solution of 75.0 g (0.125 mol; 1 eq, 2 eqof hydroxyl) of PEG 600 in 300 mL of TH dropwise via addition funnel.Internal temp was kept ˜5° C. during the addition. After completeaddition, the slightly cloudy reaction was stirred while warming to rtover 1 hr. Following this, the reaction was again cooled to ˜0° C. and asolution of 53.93 g (0.283 mol; 2.3 eq) of Tosyl chloride in 225 mL THFwas added dropwise via addition funnel, again keeping the internal temp˜10° C. during the addition. Reaction allowed to stir overnight whilewarming to rt.

Layers allowed to separate in an addition funnel, THF separated fromaqueous layer and evaporated. Residue dissolved in 600 mL EtOAc andrecombined w/aqueous from above. Shaken, separated. Organic washed 3×125mL water, then with brine, dried over MgSO₄. Stirred over the weekend.

Filtered, solvent evaporated to give a colorless oil, which was driedunder hivac rotovap 3 hrs at ˜60° C. This gave 91.95 g of a colorlessoil (81% yield). This was a typical yield for this reaction.

The reagent table includes:

Moles/ Amount Other (density, Name MW Equiv. used purity, safety, misc.)JSJ 73-078 910 102 mmol 92.75 g used crude (1 eq) Potassium 185.22 224mmol 41.5 g Phthalimide (2.2 eq) Dimethylformamide 73.09 600 mL b.p.153° C.

The procedure includes adding to a solution of 92.75 g (102 mmol; 1 eq)of JSJ 73-078 in 600 mL anhydrous DMF at rt under Ar was added 41.5 g(224 mmol; 2.2 eq) of Potassium phthalimide as a solid in 2 portions.The heterogeneous solution was then warmed slowly to 85-90° C. (internaltemp) and the rxn stirred overnight. The phthalimide slowly went intosolution and the color became more yellow. A small amount of thephthalimide wasn't consumed, remaining a solid dispersed in thereaction.

While still warm, the reaction was poured into a separate flask and mostof the DMF was evaporated (hivac at 80° C.). Any remaining solution waskept warm while the DMF was being evaporated. The resulting sludgy solidwas diluted EtOAc (˜1 L in total) and filtered. The sludge wastriturated in a smaller portion of EtOAc (200 mL) and filtered again toensure all product was recovered. Solid was triturated w/ another 200 mLEtOAc. Filtrate was then concentrated to give a yellow oil. Continuedpumping on oil under hivac at 80° C. for several hours to removeresidual DMF. This gave 57.93 g of orange-yellow oil. This was typicalyield for this reaction.

The reagent table includes:

Moles/ Amount Other (density, Name MW Equiv. used purity, safety, misc.)JSJ 73-081 860 67 mmol 57.93 g used crude (1 eq) Hydrazine, 32.05 471mmol 15 g d = 1.021 g/mL, anhydrous (7 eq) (15 mL) b.p. 113° C.Tetrahydrofuran 300 mL b.p. 66° C. Methanol 300 mL b.p. 65° C.

The procedure includes adding to a solution of 57.93 g (67 mmol; 1 eq)of crude JSJ 73-081 in 300 mL anhydrous MeOH and 300 mL anhydrous THF atrt under Ar was added 15 mL (471 mmol; 7 eq) of Hydrazine and thereaction stirred (mechanical stirring used) at rt for 1.5 hrs. After ˜45min, white solid began to form from the homogeneous solution. This wasthought to be the byproduct of the hydrazine-phthalimide reaction. Thereaction was warmed to 40° C. and stirred overnight under Ar. Thestirring became slightly more difficult as more solid formed, so thestirring was increased slightly.

The reaction appeared the same, very thick with the solid. Rxn cooled,THF and MeOH evaporated. The residue was diluted w/ EtOAc (300 mL) thenfiltered. Filtration was relatively easy, solid washed well w/ EtOAc(200 mL). Filtrate concentrated, upon which additional solid was noted.Residue diluted back in EtOAc (300 mL), giving a slightly cloudysolution (diamine may not be completely soluble in this volume ofEtOAc). Filtered, solvent evaporated, giving a yellow oil.

This oil was placed under hivac rotovap at ˜70° C. for several hours toremove residual solvents, Hydrazine, and also possibly any residual DMFbrought from the SM in the previous step.

Example 2

Example 2 Shows PEG-Amine Derived Fluorosurfactant Syntheses

A PEG-amine derived fluorosurfactant can be made by the followingprocess: 10.0 g of Krytox 157 FSH (PFPE, 6500 g/mol, 0.00154 mole) wasdissolved in 25.0-mL of FC-3283 (521 g/mol, 45.5 g, 0.0873 mole). 0.567g PEG 600 Diamine (566.7 g/mol, 0.001 mole, 0.65 mol eq.) was dissolvedin 10.0-mL of THF (72.11 g/mol, 8.9 g, 0.1234 mole). The resultingsolutions were then combined and emulsified. The resulting emulsion wasspun on a BUCHI rota-yap, at ˜75% for ˜20 hours. The crude reactionmixture was then placed in centrifuge tubes with equal volumes of DIH2O, emulsified and centrifuged at 15,000 rpm for 15-minutes. Once theemulsion was broken, the oil layer was extracted, dried with anhydroussodium sulfate and filtered over a 0.45-um disposable nylon filter. Thefiltered oil was then evaporated on a BUCHI rota-vap, model R-200 fittedwith a B-490 water bath for ˜2-hours at 70° C.

The procedure is depicted in Scheme 1:

FIG. 5 shows Ammonium Carboxylate Salt of Krytox 157 FSH 2 Wt % FC 3283without PEG amine salt (Panel A) and with PEG 600 Diammonium CarboxylateSalt of Krytox 157 FSH at 4.0% by volume (Panel B) (Flow Rates: 2000ul/hr (FC oil), 500 ul/hr (aq). The difference in the number ofcoalesced drops in the right image indicates that the PEG amine salt iseffective in stabilizing emulsions. Emulsions made with the AmmoniumCarboxylate Salt of Krytox 157 FSH 2 Wt % FC 3283 with PEG 600Diammonium Carboxylate Salt of Krytox 157 FSH co-surfactant added at4.0% by volume were shown to remain stable when reinjected into amicrofluidic channel.

Example 3

Primer Library Generation

The primer droplet library generation is a Type IV library generation.FIG. 6 shows a schematic of the primer library generation. Step 1 of thelibrary formation is to design primers for loci of interest. There areno constraints on primer design associated with traditional multiplexPCR. Step 2 requires synthesis of the primer pairs using standard oligosynthesis. After the library elements are created, the primer pairs arereformatted as droplets, where only one primer pair present in eachdroplet. Each droplet contains multiple copies of the single primer pairdirected to a single target of interest. After the droplets for eachtype of primer pair is created, the emulsions are pooled as primerlibrary. The droplet stability prevents cross-contamination of primerpairs.

Primer Library for Genome Selection

A pooled primer library can be placed onto a microfluidic device asprovided by the instant invention. Each primer library droplet followsan inlet channel that intersects with another inlet channel, which hasdroplets containing gDNA, Taq, dNTPs and any other materials needed toperform PCR. At the intersection the two inlet channels merge into asingle main channel where the two different types of droplets, i.e., theprimer library droplet and the PCR component droplets travel singularlyuntil they are coalesced. The droplets are coalesced within the mainchannel in which they are traveling, at a widened portion of the mainchannel. In addition to the widening in the channel, electrodes are usedto coalesce the droplets containing the primer libraries and thedroplets containing the PCR components. The coalesced droplets thencontinue along the same main channel and are collected onto wellcontaining plates. The droplets in the plates are subjected tothermocycling to permit PCR amplification. The amplified DNA can then besequenced by any means known in the art. The relative number ofsequencing reads from each of 20 targeted exons can be plotted usingprimer libraries against human genomic DNA.

Primer Library for Digital qPCR Method

Disposable PDMS/glass microfluidic devices were designed with regionsmaintained at 95° C., and regions maintained at 67° C. and furtherincluding interrogation neckdowns. Aqueous fluid was infused into themicrofluidic device perpendicularly to two channels flowing immiscibleoil which generated 65 pL (50 um) droplets. The aqueous fluid containedthe following reagents:

-   -   50 mM Tris/HCl (pH 8.3)    -   10 mM KCl    -   5 mM (NH4)2SO4    -   3.5 mM MgCl2    -   0.2 mM dNTP    -   0.5% Tetronics    -   0.1 mg/ml BSA    -   0.2 units per μL of FastStart Taq DNA polymerase    -   0.5 μM each of forward and reverse primers    -   0.25 μM FAM-labeled probe quenched with a 3′ BHQ1    -   1 μM Alexa Fluor 594

Serial dilutions of the pAdeasy-1 vector (Stratagene, La Jolla, Calif.)were made from 60 to 0.0006 ng/uL or from 600 copies per/droplet to0.006 copies per/droplet

The concentrations of the diluted DNA were verified by qPCR using atraditional real-time thermocycler. PCR primers and probe were designedto detect a 245 bp region of the Adenovirus genome. Droplets weregenerated at a rate of 500 per second. The channels on the microfluidicdevice conveyed the droplets through of 2 thermal zones at a 95° C. and67° C. for 34 passes which were the equivalent of 34 cycles of two stepPCR with the following cycling parameters:

1 cycle-3 min hot start

34 cycles:

95° C. for 15 seconds

68° C. for 40 seconds

PCR droplets were interrogated at specific “neckdowns” which were 100micron long regions of the microfluidic device where the channel widthand depth decreased forcing droplets into a single file. A twowavelength laser excitation and detection system was used to interrogatethe fluorescence at each of the neckdowns at cycles 4, 8, 11, 14, 17,20, 23, 26, 29, 32, and 34. A fluorescent dye, Alexa Fluor 594, provideda constant signal in each droplet that was used for droplet detectionwithout inhibiting PCR amplification efficiency or yield.

The distribution of fluorescence signal among droplets was determined asthe droplets pass through the excitation lasers (488 nm and 561 nm) atthe last interrogation neckdown (cycle 34). A bimodal distribution ofFAM fluorescence was observed for droplets with starting templateconcentrations of less than one molecule per droplet, indicating thepresence of two populations corresponding to empty droplets and dropletsthat supported amplification. A time trace of fluorescence signals fromthose droplets is readily plotted as those droplets pass one-by-onethrough the excitation lasers. For each of the Adenovirus dilutionsexamined, the percentage of PCR positive droplets was plotted versuscycle number.

Successful amplification was detected at Adenovirus concentrations aslow as 0.006 copies per drop (0.003 pg/μl). Following amplification, thedroplets collected from the microfluidic device were broken and analyzedby automated electrophoresis to confirm a product of the appropriatesize. Consistent with the fluorescence data, gel analysis showed anincrease in total product as the amount of starting material wasincreased. The observed titers were compared with the average percentageof positive reactions predicted for each starting template concentrationby Poisson statistics and by MPN (most probable number) (see Tablebelow).

TABLE 3 Comparison of Observed Amplification Distribution to PoissonStatistics and MPN. Template Concentration PCR Positive Droplets CopiesCopies per Expected per Droplet (MPN Expected (Poisson MPN Dropletadjusted)^(a) Observed (Poisson) adjusted)^(a) 0.006 0.0050 2.08% 0.60%0.49-0.51% (± 0.000082) 0.06 0.050 (± 0.00082) 11.7% 5.82% 4.76-4.95%0.3 0.25 (± 0.0041) 20.3% 25.9% 21.6-22.4% 0.6 5.0 (± 0.0082) 32.6%45.1% 38.6-39.8% 6 5.0 (± 0.082) 89.0% 99.8% 99.2-99.4% 60 50 (± 0.82)95.9%  100%      100% 600 500 (± 8.2 98.2%  100%      100% ^(a)MPNcalculation based on the 4 lowest dilutions was 0.83 ± 0.017. Adjustedvalues are within 95% confidence.

A percentage of droplets that supported amplification was plotted versusstarting copy number compared to that predicted by Poisson. Very goodagreement was seen between the percentage of droplets that supportedamplification and the predicted Poisson distribution. Given the accuracyof the data for endpoint analysis this droplet-based strategy appears tobe ideal for quantitative PCR applications that require single moleculedetection.

Example 4

Generating Single Element Droplets

As described in detail herein, the formation of Type II librarydroplets, which encapsulate a library element, e.g., cell or bead,follow a Poisson Distribution. Using the following, equation, thedistributions were calculated based on theory using the followingequation:P(N)=((CV)^(N) e ^(−CV))/N!

where P is the probability of N particles per drop, C is the injectionconcentration, and V is the droplet volume.

Experimental results are based on beads that were injected at aconcentration of 40 million/ml into 23 μm drops (6.37 pL); CV=0.2548.The results are shown in the following table:

Theoretical Experimental # of Drops P(N) Poisson DistributionDistribution Counted P(0) 77.5 79.8 1010 P(1) 19.7 17.3 219 P(2) 2.5 2.532 P(3 and more) 0.3 0.4 5 Total 100% 100% 1266

Example 5

Antibody-Bead Libraries—ELISA in Droplets

The primer droplet library generation is a Type II library generation.FIG. 3 shows a schematic of the antibody pair library generation.Reagent solutions 1 through n, where n is the number of parallel ELISAassays to be performed, are prepared in separate vials. Each solutioncontains two antibodies, one bound to beads and one free in solution. Itis often desirable, but not essential, for the unbound antibody to bebiotinylated or for it to be conjugated to an enzyme. The beads areoptically labeled using dyes, quantum dots or other distinguishingcharacteristics that make each of the n bead types uniquelyidentifiable, these characteristics can be also geometrical shape orfeatures or fluorescence intensity or fluorescence polarization. For theemulsion library preparation: in separate locations, beads of each typeare encapsulated in reagent droplets; the reagent contains an unboundsecond antibody matched for a specific immunoassay. It is oftendesirable, but not essential to have exactly one bead in a droplet.Droplets having exactly one bead are collected by sorting on dropletgeneration in a microfluidic device. The emulsion library consists of apooled collection of the n different droplet types. The dropletstability prevents cross-contamination of antibody pairs.

FIG. 3 shows the test fluid is the sample fluid used to analyze one ormore immunoassays. Example test fluids include serum, sputum, urine ortumor biopsies. In step 1 the test fluid is dispersed into droplets ofuniform volume and combined with a single droplet from the library.There may be unpaired droplets of the library material. In step 2 thebeads are recovered, washed in bulk, a readout enzyme is introduced.Non-limiting examples of readout enzymes could include a conjugatestreptavidin-enzyme (typical enzymes are, for example but not limitedto: β-Galactasidase, alkaline phosphatase, horseradish peroxidase), orconjugate antibody-enzyme (for example the same list of enzymes),followed by a final wash. In step 3 the beads are put back onmicrofluidic device at a low concentration so that limiting dilutionconditions result. Most droplets will contain zero beads and mostbead-containing droplets will have only one bead. Droplets containingexactly one bead will be used for the remainder of the assay. Dropletswith no beads or more than one bead are sorted and discarded asdiscussed above. A fluorogenic substrate is added to the droplets underco-flow conditions at the time of droplet generation. The substrate isenzymatically turned-over to make a fluorescent product proportional tothe concentration of analyte (and readout enzyme) in the sample fluid.An optical signal indicating the bead type and immunoassay numberinformation is read on the beads simultaneously with the fluorescencesignal from the product. This is done at one or more time points afterthe droplet is generated. Bead handling may benefit from using magneticbeads.

In some cases it may be advantageous to enhance step one with a sortprocedure to remove the droplets containing excess beads that have nothad the test fluid added to them. The sort can be triggered either bydroplet size or through the introduction of a fluorescent dye to thetest fluid.

In some cases it may be advantageous to collect all beads on-chip. Thisis achieved with a micro-fabricated bead filter. Beads can then bewashed, introduced to additional reagents, and subsequently followed bya final wash. By performing all of the previous steps all on-chip, theneed for bulk processing of beads is eliminated.

In some cases it is difficult to re-space beads after the final wash ofstep 1. In those cases it may be advantageous to capture beads inisolation on-chip. In the example, the substrate is added in bulk andthe diffusion of the product around the bead is measured. There areseveral other non-limiting examples of methods that could also beapplied in a microfluidic device. For example, one could use a tyramideamplification assay.

Auto-loading of sample fluids, injection loop and dispense techniquescan be utilized to enhance efficiency. Test fluids can be runsequentially using conventional auto-loaders and sample injection loops.Each sample would need to be separated by a rinse fluid and the off-chipprocessing of beads would require that the beads from each test fluid becollected separately.

Droplet ELISA Performance—Reported Enzyme

The activity of reporter enzyme bound to single positive beads(anti-m-biotin) or single negative beads in 30 um droplets can beassayed with HorseRadish Peroxidase (HRP) enzyme. Under the assayconditions, the beads were injected at a final concentration 10million/ml, HRP readout at 10 minute time point—Amplex Ultra Red 100 uM,hydrogen peroxide 1 mM. HRP allows for adequate separation of beadcontaining droplets from empty droplets. Additionally, a linear responseis seen down to 10 molecules in a 30 um drop (at 10 minutes).

Droplet ELISA Performance—Binding

Similar binding kinetics are seen when performing ELISA in a tube whencompared to performance in droplets. Specifically, similar bindingkinetics and a linear calibration curve is seen using droplets.

Droplet ELISA Performance—Full Assay

Serum concentration can be measured accurately and is able to bereproduced, generally within a CV of less that 6% as shown in the Tablebelow that shows the results of serum sample replicates (˜60,000droplets/run)

Antigen t = 0 min t = 10 min pg/ml All drops Empty drops Bead dropsHuman serum 18.2 21.7 252 1:1600 Human serum 19.7 25.8 264 1:1600 Humanserum 23.5 25.6 278 1:1600 Positive control 20.5 56.2 4272 beads

Example 6

Sorting Cells for Secreted Enzymatic Activity

Molecular biology methods allow for generation of large libraries ofmutant enzymes, which can be cloned DNA, which can be developed into amutagenized DNA library that is then put into a bacterial host. Thedroplet based screening is high-throughput, highly accurate and has lowreagents costs. The droplets provide an accurate high-throughput screenversus a halo assay. Specifically, the DNA enzyme contained within thebacterial host is encapsulated within a droplet that also contains afluorogenic substance, creating a droplet library of the bacteria, whereonly a single bacteria is contained with the droplets. All droplets,however, contain the fluorogenic substrate. After the droplet library iscreated the bacteria are allowed to replicate for a set time period,i.e., overnight. Using a green filter shows the discrete bacteria,within particular droplets, and using a red filter shows the secretedenzyme.

Droplet libraries can also be used in enzyme activity detection withsingle cell growth and enzyme secretion. A droplet library can include anumber of droplets containing a single cell, where other droplets do notcontain any cells. The cells remain in the droplets overnight and growinto clonal populations. Both the discrete bacteria and the secretedenzyme are detected with an overlay of assay and cell fluorescence. Thedroplet library is then sorted, such that the droplets all contain aclonal population of bacteria having secreted the desired enzyme. Thedroplet library enables a single cell generation to result in clonalpopulations within single droplets to be used in assays and or to besorted.

Activity in droplets is similar to that seen in microtitre plates.Matching rank orders with microtiter plate assays and droplet assaysshow similar rank orders using either method.

Cell droplet libraries enable the sorting of the most active stain froma mixed cell library. In one example, droplets were generated with fourindividual strains and optical labeling using specific fluoresceinconcentrations (labeling plotted on y-axis). All of the droplets werecollected into the same syringe and the mixed droplets were re-injectedonto a microfluidic device after overnight growth at 30° C. A scatterplot shows the four labeled populations of droplets starting with noassay signal (on generation), and droplets having growing cellssecreting protease showing assay activity moving to the right (after 16hrs). The origin of each droplet is clearly identified, with the assaysignal strength for each droplet type matching the appropriate strainranking. Starting from a dilution of 1 positive in 100 Negatives viablebacteria can be recovered from sorted droplets to achieve sortedpopulation.

In another example, a 5-member library sorting can be achieved. Astarting ratio of one Pos #4-containing droplet to 30 cell-containingdroplets was used. Pos #3 cells only are kanamycin resistant. Afterrecovering and plating out the contents of the sorted droplets, therewere 19 kanamycin-resistant colonies out of 1131 total colonies. This isequivalent to an apparent false positive rate of 1.7%.

Sorting the most active strain can also be done with large (i.e., 2million members) mixed cell libraries. Further exemplified is a parentlibrary of 2×10⁶ discrete cell types (bacteria secreting mutagenizedenzyme library) was placed into droplets for growth and screening. Twolevels of sorting threshold stringency were used to recover either thetop 100 cells or the top 10K cell. After re-growth, each population wasplaced in droplets for an enriched library analytical run. Threepopulations were optically labeled, and five minutes of data werecollected after cell growth and assay development in droplets. Clearenrichment of the parent library is seen in the Top 10K-EnrichedLibrary. Validation of Test Library #1 enrichment is seen. White and redfiltered microscope images of the Parent Library (Test Library #1) indroplets after growth are observed. Similar images of the Top10K-Enriched Library are seen. Clear enrichment for active clones arealso observed.

Example 7

Sorting Cells for Biomarkers Using Enzyme Amplification—Flow Cytometry

FIG. 7 shows a schematic of the encapsulation of enzyme labeledindividual cells in a substrate containing droplets. In contrast,traditional flow cytometry utilizes fluor-labeled antibodies. Thecontents of the droplets are then amplified, such that the contents ofthe droplet produce a labeled product. The contents are then put ontothe microfluidic device in order to sort/recover the desired products.

A particular example is the U937 Monocyte Droplets, where cell libraryof an antibody, reporter enzyme and cell stain is prepared and co-flowedinto droplets with the assay substrate. Depending on the contents of thedroplet, a different signal is produced and the number of cells perdroplet follows a Poisson distribution, where 8.4% of the droplets havea single cell, i.e., 25356 single cell droplets out of 300943 totaldroplets. Additionally, the enzyme amplified signal increases over time.The droplet libraries also enable multiplexed assays with opticallabeling. Various labels can be utilized and overlayed. In a comparisonof FACS and droplet sorting, droplet sorting provides improved cellpopulation fractionation.

Example 8

Cell Libraries—Bacterial Libraries for Antibody Screening

Screen libraries of bacterially produced scFv's can also be developed.In one example, transformed bacteria are encapsulated and incubated at37° C. After incubation the droplets are combined with droplets thatcontain beads, antigens and a detection antibody. After the twodifferent droplets are combined they are collected and sorted. Thepositive droplets are then broken and the contents are recovered andsequenced. The process is able to screen for scFv's in droplets at arate of about 1×10⁶ per hour. The droplet based binding assays utilizelocalized fluorescence detection of scFV binding. Specifically, thediffuse signal becomes bright and localized on the capture bead.

Example 9

Compound Libraries—Screening for Inhibitor Enzymes

The present invention provides Immobilized Metal-Ion AffinityPartitioning (IMAP) FP detection of kinase reaction progress.Significant achievements allowing the instant method include:

Solving problems handling IMAP, such as precipitation and providingproper mixing.

Fast mixing/equilibrium in droplets allows direct on-chip analysis.

Initially, a significant precipitation of the IMAP particles in thesyringe, particularly when present at high concentrations was observed.A mechanical mixing device and protocols was utilized to minimize thisproblem. Subsequently, this problem was fully solved by varying theratio of buffers provided in Molecular Devices' Progressive BindingBuffer system, with a final concentration of 50% A:B buffer used for allassays. Buffer B contains a high salt concentration which preventedaggregation, and in addition allows a single buffer system to be usedfor many different kinases (using different substrates with a range ofacidity).

There are several distinct steps in performing kinase assays withindroplets. First the reaction components are encapsulated inside dropletsgenerated by a microfluidic device and collected into a syringe. Next,the refrigerated syringe is brought up to the reaction temperature, andthe ‘emulsified’ reaction mixture proceeds to react for a defined amountof time. Finally, the reaction emulsion is re-injected and eachindividual droplet is analyzed when it flows past a laser detector. Inthis scheme, detection of the phosphorylated reaction product is viameasurement of its Fluorescence Polarization (FP) after binding to thecommercially available Immobilized Metal-Ion Affinity Partitioning(IMAP) kit reagents (Molecular Probes). The scheme incorporates aformulation step allowing chemical compounds to be tested for theirinhibitory properties towards kinases. The fluorescence polarization ismeasured for each droplet and changes upon binding. Specifically, thephosphorylated product binds to IMAP and increases its FP. Compound/DMSOdilution and encapsulation of the reaction reagents into droplets isformulated on the microfluidic device.

In one example, two sets of droplets are initially generated, one froman aqueous stream made of compound (provided in 70% DMSO) and ATP(nozzle 1), and the other from an aqueous stream containing the kinaseand substrate in a reaction buffer (nozzle 2). These two droplet typesare subsequently coalesced via the application of voltage from theelectrode, generating the final reaction mixture droplets which iscollected into a glass syringe.

When generating the compound/ATP droplets, fluid flow rates are set suchthat the compound that is initially in 70% DMSO is diluted to aconcentration of 10% DMSO in the droplets generated by nozzle 1. Thevolume ratio of droplets generated at nozzle 1 vs. nozzle 2 is 1 to 3,therefore when droplets from nozzle 1 are coalesced with droplets fromnozzle 2 (containing the kinase and substrate) there is another 4 folddilution of DMSO is therefore 28-fold (the concentration of DMSO in thefinal reaction mix is 2.5%).

Coalescence of droplets with IMAP, IMAP binding, and timed readout ofdroplets are observed. Specifically, IMAP particles are encapsulatedinside droplets which are subsequently coalesced with the emulsifiedreaction mixture droplets as they are being re-injected. The dropletsenter a delay line which provides sufficient time for each droplet to beinterrogated using an FP readout as it moves from left to right throughthe microfluidic channel shown.

A combined microfluidic device design was also developed in order toimprove emulsion stability (by reducing microfluidic device connectionmanipulations) and to reduce the time required for switchingmicrofluidic devices and re-equilibrating fluid pressures. In thisdesign, the same channel is used for both emulsion collection andre-injection, allowing for emulsion generation, IMAP coalescence and FPreadout all on one microfluidic device. This design provides for ahigher degree of automation and reproducibility by reducing operatormanipulations of the microfluidic devices and optics, reducingopportunities for contaminants to be introduced into the microfluidicsystem, and provides better control of the operation time.

In order to generate kinetic data on the kinase reaction progress, acollection of the reaction droplet emulsion at 4° C. was provided, toprevent the enzymatic reaction from proceeding until the temperature israised. Once the emulsion has been generated, the syringe can be raisedto any temperature desired (e.g. room temperature or 30° C.). All of theexperiments shown in this report were performed at room temperature.Time course experiments were also performed by varying the time that theemulsion was kept at room temperature, before re-injection andcoalescence with the IMAP detection reagent. Automated protocols wereestablished allowing for time points to be collected every 10 minutesover a period up to 4 hours.

Optical components have been defined and developed to enable FPdetection. Optical components were assembled, using a 25-milliwattsolid-state laser to generate a 10 micron focused laser spot in themicrofluidic channel, allowing a fluorescence signal to be measured foreach droplet. The prototype instrument used in this study is able todetect approximately 10,000 FITC molecules encapsulated in a 30 microndroplet passing through the detection point at a rate of up to 10,000per second.

Binding of the IMAP particle to the phosphorylated peptide substrate canbe directly observed using the microfluidic device. As each dropletmoves at a defined flow rate through the circuitry, observation atdifferent positions after IMAP coalescence defines specific times afterbinding. A delay line allows measurements over approximately 20 secondsafter binding IMAP. Binding of the Akt positive control phospho-peptideto IMAP and the reaction of Abl-tide substrate with Abi kinase are seen.Binding of the IMAP reagent to both of these phospho-peptides reachesequilibrium within 10 seconds. Further, a comparison of on-chip andplate reader assays using 3 compounds where % inhibition time coursesfor Abl kinase and compounds E, A, and H show improved resolution foron-chip assays.

Example 10

Compound Libraries—Screening for Cytotoxic Drugs

In one example, one nozzle is used to encapsulate U937 mammalian cellsthat are cultivated in RPMI supplemented with fetal calf serum (10% v/v)under saturated CO₂ atmosphere (5%). Flow-focusing geometry to form thedroplets was used. A water stream is infused from one channel through anarrow constriction; oil streams hydrodynamically focus the water streamand reduce its size as it passes through the constriction resulting in a“geometry-controlled” breakup of the droplet. The size of the waterdroplets is controlled in part by the relative flow rates of the oil andthe water and in part by the nozzle section dimensions. The fluorinatedoil contains a fluorocarbon surfactant (Ammonium Carboxylate Salt ofPerfluoropolyether, 1% w/w) to stabilize the droplets. Cell density uponinjection with discussion on Poisson's distribution and single cellanalysis % drop size. Pluronic F-68 (0.1% final solution) ashear-protectant, is added to the cells just prior the injection tominimize the effect of shear-stress. The other nozzle generates dropletscontaining the Calcein-AM and Sytox Orange (Invitrogen) dyes that areused to respectively score live and dead cells. In brief, Calcein-AM ismembrane permeant, non-fluorescent and diffuses into cells where theacetoxy groups are hydrolyzed by nonspecific esterases. The hydrolyzeddye (Calcein) is both cell membrane impermeant and fluorescent. SytoxOrange is impermeant and excluded from viable cells, but is able toenter cells with compromised membranes. In this case, it binds to DNA byintercalating between the bases with little sequence specificity and itsfluorescence is greatly enhanced. Finally, a fluoro-surfactant(Zonyl-FSO, 1.3%, Dupont) was added in the dye solution to prevent theinteraction of the dyes with the carboxylate group of the mainsurfactant. The droplet streams are interdigitated so that each celldroplet pairs with a dye droplet before entering the coalescence module.To this end, the fact that smaller droplets flow at higher velocitiesthan larger droplets due to the parabolic flow velocity distribution inmicrofluidic channels was exploited. The small dye droplets catch up andcome into contact with the larger cell droplets, but do not coalescebecause they are stabilized with surfactant. In addition, in order tohave each cell droplet paired with a dye droplet the formation rate ofdye droplets is higher than the formation rate of cell dropletsformation in a ratio close to 1:2. Coalescence is controllably inducedwhen a pair of droplets passes through an alternative electric field(˜300V·cm⁻¹, 100 kHz). The expansion in the coalescing region allows fora dramatic catching up of the small droplet to the large droplet andaccounts for a very robust coalescence (fewer than 0.1% misses). Thevolume of the expansion is big enough to slow the large droplet down sothat the small droplet always catches up to the large droplet, butdoesn't allow the next droplet to catch up and make contact with thepair to be coalesced. After the droplet pairs are coalesced, theircontent, i.e. cells and dyes, is mixed by traveling through a passiveserpentine mixer. Because the Calcein-AM dye has to be processedenzymatically by the cells to become fluorescent, the droplets need tobe incubated on-chip for tens of minutes. To achieve this type ofincubation on-chip the cross-section (600 μm×250 μm) and the length ofthe channel (1,550 mm) was increased so that the flow sweeps through alarge volume. This design results in a significant residence time on themicrofluidic device. In addition, to modulate with ease the incubationperiod without changing the flowrates used for generating the dropletsoil from the flowing stream was extracted. The oil extractor consists ofa series of T-junction whose sections are much smaller than the dropletsize, which are used to specifically extract oil and reduce the overallflowrate and hence the droplet velocity. The combined use of theincubation line and the oil extractor results in a significant on-chipresidency time of the droplets. Typically, the live-dead assayexperiments are carried out with an incubation time of 70 minutes on themicrofluidic device. For consistent fluorescent detection, all the cellsare illuminated in the same conditions by confining them through aconstriction and by using a slit geometry for the excitation spot. Aconfocal optical set-up is used and the signal is collected with a setof photomultipliers at a rate of 100 kHz.

A typical fluorescent readout is provided, over a timescale of 100 ms.The cell growth medium gives a dim fluorescent background which is muchlower than the live-dead assay signals. To compensate for this lowsignal, some fluorescein (10 μM) (Invitrogen) was added into the dyesolution to get a clear fluorescent signature of the droplets which ischaracterized by an approximately rectangular cross-section. Peaksignals corresponding to cell staining are characterized by highermaximum signal and narrower Forward Half Maximum. They can be clearlydistinguished on top of the homogeneous signal. Data processing softwarehas been developed to extract different parameters (height, integratedarea . . . ) after interpolation and curve fitting from each dropletsignal. After scoring the cells retain a normal morphology without anyapparent sign of shearing. Cell density upon injection with discussionon Poisson's distribution and single cell analysis % drop size.

To test the performances of the assay, a series of experiments wereconducted to test its specificity and its sensitivity. First, the signalspecificity was checked by injecting and scoring with the live-deadassay either only live or dead cells. Dead cells were prepared byincubating fresh cells with 70% Ethanol for 5 minutes. The experimentdemonstrates that the assay is very specific as all the cells are scoredproperly. In addition, it shows that the injection does not kill thecells over a short-term period, in agreement with other's observations.

Second, the assay was test to see whether it was able to score all theinjected cells disregarding their cell state (either alive or dead). Tothis purpose all the cells with a red dye (QDOT 655 wheat germagglutinin, Invitrogen) were identified and checked that they were allscored. Again, live cells and dead cells were scored separately. It isnoteworthy that these numbers are the result of the combinedefficiencies of all the modules used for the live-dead assay,demonstrating the robustness of this assay and technology.

Third, to assess the usefulness of this assay for screening purpose aseries of known ratios of live and dead cells were scored in the rangeof 0-10% dead cells. Indeed, the fraction of positive hits for acytotoxicity large-scale screen is expected to be in the order of a fewpercent. For example, as little as 5% positive cells can be reproduciblydetected in a sample population of 500-1,000 measured cells.

Finally, it was demonstrated that encapsulated cells can be collectedinto a syringe and the emulsions re-injected for on-chip scoring. Thisability is an essential feature of the technology for conductingscreens, as the cells will have to be incubated with compounds for amuch longer time than achievable on-chip.

It was observed that the cell emulsion which is re-injected through thelower nozzle is still monodisperse. The stability depends critically onthe use of the fluoro-surfactant and design of the microfluidic circuitto avoid uncontrolled coalescence. By the use of a scatter plot, it isdetermined that most of the cells are able to survive thecollection-reinjection procedure.

The droplet microfluidic technology will facilitate an expansive list ofmicrofluidic applications. In particular high-throughput cell screeningand combinatorial screening at the single cell level will greatlybenefit from this technology platform. The major advantages of thistechnology are the absence of contact between the sample and the channelwalls eliminating contamination, and high-throughput manipulation.

The toxicity assay with droplets requires encapsulating cellsdetermining the difference between live cells and dead cells. In orderto get a reading of the droplet and fluorescent level therein, thedroplet is elongated for detection. The cell viability does notsignificantly change over time (>3 days) in the droplets.

What is claimed is:
 1. A method of performing a digital ELISA assay indroplets, the method comprising: providing reagent droplets comprisingreporter antibodies and second antibodies bound to magnetic beads into achannel of a microfluidic device; introducing test droplets comprising atest fluid into the microfluidic device; combining the reagent dropletswith the test droplets in the microfluidic device to form ELISAsandwiches, each ELISA sandwich comprising one bead-bound antibody, atarget analyte from the test fluid, and one reporter antibody; adding,via the microfluidic device, a fluorogenic substrate into droplets thatcontain one of the ELISA sandwiches; and detecting fluorescenceindicating presence of the target analyte, wherein the detecting stepprovides a digital count of a number of molecules of analyte per volumeof the test fluid.
 2. The method of claim 1, wherein the reporterantibodies are provided as biotinylated antibodies.
 3. The method ofclaim 2, further comprising introducing a streptavidin-linked enzyme foruse in forming the ELISA sandwiches.
 4. The method of claim 3, whereinstreptavidin-linked enzyme comprises streptavidin beta-galactosidase. 5.The method of claim 1, wherein the fluorogenic substrate comprisesfluorescein di-beta-D-galactopyranoside (FDG).
 6. The method of claim 1,wherein the target analyte comprises a protein, the detecting stepyields a digital count of individual molecules of the protein pervolume, and the method further comprises quantifying the protein in thetest fluid from the digital count.
 7. The method of claim 1, wherein thedetecting step comprises reading a first optical signal indicating thebead type and the fluorescence signal indicating the presence of thetarget analyte.
 8. The method of claim 1, wherein after the ELISAsandwiches are formed, the method includes retaining the magnetic beadsby a magnetic field while removing unbound non-target proteins and freeantibodies, prior to adding the fluorogenic substrate.
 9. The method ofclaim 1 wherein the droplets containing the one ELISA sandwich areformed and—after the droplets containing the one ELISA sandwich areformed—the fluorogenic substrate is added.
 10. The method of claim 1,further comprising—after forming the droplets—sorting droplets anddiscarding droplets with no beads or with more than one bead.